Clasificación de protistas

Una interpretación moderna no jerárquica de la filogenia de los eucariotas, incluidos los protistas (la línea gris sin etiquetar junto a Sar representa Telonemia ).

Un protista ( / ˈ p r oʊ t ɪ s t / ) es cualquier organismo eucariota (uno con células que contienen un núcleo) que no es un animal , una planta o un hongo . Los protistas no forman un grupo natural, o clado , ya que excluyen a ciertos eucariotas con los que comparten un ancestro común; ^[^a^] pero, al igual que las algas o los invertebrados , la agrupación se usa por conveniencia. En algunos sistemas de clasificación biológica , como el popular esquema de cinco reinos propuesto por Robert Whittaker en 1969, los protistas conforman un reino llamado Protista , compuesto por "organismos que son unicelulares o unicelulares-coloniales y que no forman tejidos ". ^[¹^]^[^b^] En el siglo XXI, la clasificación cambió hacia un sistema de dos reinos de protistas: Chromista (que contiene los grupos cromalveolados , rizarios y otros) y Protozoa (que contiene excavados y todos los protistas más estrechamente relacionados con animales y hongos). ^[²^]

Los siguientes grupos contienen protistas. El clado Opisthokonta también incluye a los animales y los hongos, y Archaeplastida también a las plantas.

Leyenda:

† Taxón extinto o exclusivamente fósil.

^(P) Taxón parafilético o polifilético.

^(P?) Taxón potencialmente parafilético o polifilético.

(=...) Sinónimo taxonómico.

(...) El mismo taxón en un código de nomenclatura diferente.

Amorfea

El supergrupo Amorphea contiene organismos heterótrofos muy diversos, desde hongos y animales macroscópicos hasta coanoflagelados unicelulares y amebas clásicas . Con frecuencia presentan la capacidad de producir células multinucleadas, un rasgo considerado ancestral de Amorphea. También son capaces de producir pseudópodos , al igual que el clado CRuMs , estrechamente relacionado , formando el clado Podiata . ^{[ 3 ]}

Amorphea se divide en dos clados: Amoebozoa , que contiene amebas y mohos mucilaginosos bien conocidos, y Obazoa , que contiene animales, hongos y sus parientes más cercanos. La relación entre estos dos clados se denominó inicialmente "Unikonta", debido a una hipótesis que planteaba que su ancestro común era un unikonte, es decir, un eucariota con un solo flagelo. ^{[ 4 ]} Sin embargo, esta hipótesis fue refutada, ya que existen amorpheos bikontos (por ejemplo, Breviata anathema ) y es probable que tener un solo flagelo no sea un rasgo ancestral. ^{[ 5 ]}^{[ 6 ]}

Obazoa

El clado Obazoa contiene dos pequeños grupos de flagelados, los breviados y los apusomónadas , y el gran clado Opisthokonta , que contiene animales, hongos y sus parientes protistas más cercanos. ^{[ 10 ]} Bajo el sistema Cavalier-Smith, los breviados y los apusomónadas eran dos clases que componían el filo Apusozoa , ^{[ 11 ]} pero este taxón es parafilético, ya que los apusomónadas están más estrechamente relacionados con los opistocontos. ^{[ 7 ]} La taxonomía de los apusomónadas se amplió en un estudio filogenético de 2022 que introdujo muchos géneros nuevos. ^{[ 12 ]}

Clase Breviatea Cavalier-Smith 2004 , orden Breviatida Cavalier-Smith 2004. Género no asignado a ninguna familia: Lenisia .
- Familia Breviatidae Cavalier-Smith 2013 , géneros Breviata , Subulatomonas .
- Familia Pygsuidae Cavalier-Smith 2022 , género Pygsuia .

Clase Thecomonadea Cavalier-Smith 1993 emend. 2013 , orden Apusomonadida Karpov & Mylnikov 1989 , familia Apusomonadidae Karpov & Mylnikov 1989. Géneros no asignados a ninguna subfamilia: Amastigomonas , Multimonas , Podomonas , Catacumbia , Cavaliersmithia , Karpovia , Singekia .
- Subfamilia Apusomonadinae Cavalier-Smith 2010 , géneros Apusomonas (= Rostromonas ), Manchomonas .
- Subfamilia Thecamonadinae Larsen & Patterson 1990 , géneros Chelonemonas , Thecamonas .

Opistokonta

Los opistocontos se dividen en dos ramas: Holozoa (relacionados con los animales), que incluye a los ictiosporidios , pluriformes , filastereos y coanoflagelados ; y Nucletmycea u Holomycota (relacionados con los hongos), que incluye a los nucleidos y opistosporidios . Estos grupos, excepto los opistosporidios, se clasificaban como clases diferentes dentro del filo parafilético Choanozoa en el sistema de Cavalier-Smith, ahora obsoleto. En cambio, Choanozoa es el nombre que se usa para el clado que incluye a los coanoflagelados y a los animales. Los opistosporidios (afélidos, rozelidos y microsporidios) a menudo se estudian como protistas, pero también son considerados hongos por protistólogos ^{[ 10 ]} y micólogos por igual. ^{[ 13 ]} Tanto Holozoa como Nucletmycea han sido propuestos una vez como superreinos por un grupo de micólogos que clasificaron a los nucleidos y los hongos como reinos, pero sin ninguna mención de los reinos holozoos. ^{[ 14 ]}

Nucletmicea Brown et al. 2009 (=Holomycota Liu et al. 2009 )
- Orden Rotosphaerida Rainer 1968 (=Cristidiscoidida Página 1987 ), familia Nucleariidae Cann & Page 1979 (=Pompholyxophridae Página 1987 ), géneros: Fonticula , Nuclearia , Parvularia , Pompholyxophrys , Lithocolla , Vampyrellidium , Elaeorhanis , Pinaciophora , Rabdiophrys , Rabdiaster , Thomseniophora . ^{[ 15 ]}
- Reino Fungi R.T. Moore 1980
Holozoa Lang et al. 2002 . Genera incertae sedis : Tunicaraptor , ^{[ 8 ]} † Bicellum . ^{[ 16 ]}
- Clase Ichthyosporea Cavalier-Smith 1998 (=Mesomycetozoea Mendoza et al. 2002 )
  - Orden Dermocystida Cavalier-Smith 1998 , familia Rhinosporidaceae Mendoza et al. 2001 , géneros Amphibiocystidium , Amphibiothecum , Chromosphaera , Dermocystidium , Rhinosporidium , Sphaerothecum , Valentines . ^{[ 17 ]}
  - Orden Ichthyophonida Cavalier-Smith 1998 (=Ichthyophonae Mendoza et al. 2001 ), familia Amoebidiidae Reeves 2003 , géneros Abeoforma , Amoebidium , Anurofeca , Astreptonema , Caullerya , Creolimax , Eccrinidus , Enterobryus , Enteropogon , Ichthyophonus , Palavascia , Pseudoperkinsus , Psorospermium , Sphaeroforma .
- Pluriformea Hehenberger et al. 2017
  - Familia Corallochytriidae Cavalier-Smith en Cavalier-Smith & Allsopp 1996 , género Corallochytrium Raghu-Kumar 1987 .
  - Familia Syssomonadidae Cavalier-Smith 2022 , ^{[ 18 ]} género Syssomonas .
- Clase Filasterea Shalchian-Tabrizi et al. 2008 , orden Ministeriida Cavalier-Smith 1997. Género no asignado a ninguna familia: Pigoraptor .
  - Familia Ministeriidae Cavalier-Smith 1997 , género Ministeria .
  - Familia Capsasporidae Cavalier-Smith 1997 , género Capsaspora .
  - Familia Txikisporidae Urrutia, Feist & Bass 2022 , género Txikispora . ^{[ 19 ]}
- Choanozoa Brunet & King 2017
  - Clase Choanoflagellata Kent 1880–1882 (=Craspedomonadina Stein 1878 , Craspedomonadaceae Senn 1900 , Craspedophyceae Chadefaud 1960 , Craspédomonadophycidées Bourrelly 1968 , Craspedomonadophyceae Hibberd 1976 , Choanomonadea Krylov et al. 1980 , Choanoflagelliida Lee, Hutner & Bovee 1985 , Choanoflagellatea ^Cavalier^-^Smith 1997 enmienda Cavalier-Smith 1998 ^, Choanomonada ^Adl^et al .
    - Orden Craspedida Cavalier-Smith de 1997 modificada. Nitsche et al. 2011 , enmienda de la familia Salpingoecidae Kent 1880–1882 . sensu Nitsche et al. 2011 (=Codonosigidae Kent 1880–1882 ), géneros Astrosiga , Aulomonas , Barroeca , ^{[ 22 ]} Choanoeca , Cladospongia , Codonocladium , Codonosigopsis , Codosiga (= Codonosiga ), Desmarella (= Codonodesmus , Kentrosiga ), Dicraspedella , Diploeca , Diplosiga , Diplosigopsis , Hartaetosiga , Kentia , Lagenoeca , Microstomoeca , Monosiga , Mylnosiga , Pachysoeca , Proterospongia , Salpingoeca , Salpingorhiza , Sphaeroeca , Stagondoeca , Stelexomonas , Stylochromonas .
    - Orden Acanthoecida Cavalier-Smith de 1997, enmendada. Nitsche et al. 2011
      - Familia Acanthoecidae Norris 1965, enmienda. sensu Nitsche et al. 2011 , géneros Acanthoeca , Enibas , ^{[ 23 ]} Helgoeca , Polyoeca , Savillea .
      - Familia Stephanoecidae Leadbeater 2011 , géneros Acanthocorbis , Amoenoscopa , Apheloecion , Bicosta , Calliacantha , Calotheca , Campanoeca , Campyloacantha , Conion , Cosmoeca , Crinolina , Crucispina , Diaphanoeca , Didymoeca , Kakoeca , Monocosta , Nannoeca , Parvicorbicula , Thomsenella (" Platypleura "), ^{[ 24 ]} Pleurasiga , Polyfibula , Saepicula , Saroeca , Spinoeca , Spiraloecion , Stephanacantha , Stephanoeca , Syndetophyllum .
  - Reino Metazoa Haeckel enmienda de 1874. Adl et al. 2005 (=Animalia Linneo 1758 )

Amebozoa

El filo Amoebozoa contiene alrededor de 2400 especies ^{[ 26 ]} de protistas principalmente ameboides. ^{[ 10 ]} Incluye una gran parte de los Sarcodina tradicionales, el taxón que une a todas las amebas. En particular, agrupa a las amebas lobosas desnudas y testadas (las Lobosa tradicionales ), así como a las arqueamoebas y los eumicetozoos (mohos mucilaginosos), y algunos flagelados. ^{[ 27 ]} Después de las revisiones generales de 2019 publicadas por la Sociedad Internacional de Protistólogos (ISOP), ^{[ 10 ]} ha habido revisiones específicas a la clasificación de los eumicetozoos ^{[ 28 ]} y las amebas testadas. ^{[ 29 ]}

Filo Amoebozoa Lühe 1913 sensu Cavalier-Smith 1998 . Géneros incertae sedis : Belonocystis , Boveella , Biomyxa , Corallomyxa , Gibbodiscus , Hartmannia , Malamoeba , Malpighamoeba , Oscillosignum , Pseudothecamoeba , Rhabdamoeba , Schoutedamoeba , Stereomyxa , Subulamoeba , Triaenamoeba , Unda . ^{[ 10 ]}

Clase Tubulinea Smirnov et al. 2005
- Coricuria Kang et al. 2017 ^{[ 30 ]}
  - Orden Trichosida Möbius 1889 , familia Trichosphaeriidae Sheehan & Banner 1973 (=Trichosidae Möbius 1889 ), género Trichosphaerium (= Atrichosa ).
  - Familia Microcoryciidae de Saedeleer 1934 , géneros Amphizonella , Diplochlamys , Microcorycia , Parmulina , Penardochlamys , Zonomyxa . ^{[ c ]}
- Orden Echinamoebida Cavalier-Smith et al. Enmienda de 2004. Smirnov et al. 2011
  - Familia Echinamoebidae Page 1975 , géneros Echinamoeba , Micriamoeba .
  - Familia Vermamoebidae Cavalier-Smith & Smirnov 2011 , género Vermamoeba .
- Elardia Kang et al. 2017 ^{[ 30 ]}
  - Orden Leptomyxida Pussard & Pons 1976 emend. Page 1987
    - Familia Leptomyxidae Pussard & Pons 1976 , género Leptomyxa .
    - Familia Rhizamoebidae Smirnov et al. 2016 , género Rhizamoeba . ^{[ 31 ]}
    - Familia Flabellulidae Bovee 1970 , género Flabellula ^{[ 32 ]} (= Paraflabellula ).
    - Familia Gephyramoebidae Pussard & Pons 1976 , género Gephyramoeba . ^{[ 31 ]}
  - Superorden Eulobosia Cavalier-Smith et al. 2016
    - Orden Euamoebida Lepşi 1960 sensu Smirnov et al. 2011
      - Familia Amoebidae Ehrenberg 1838 Página 1987 , géneros: Amoeba , Chaos , Polychaos , Parachaos , Trichamoeba , Deuteramoeba , Hydramoeba .
      - Familia Hartmannellidae Volkonsky 1931 , géneros Cashia , Copromyxa , Copromyxella , Glaeseria , Hartmannella , Ptolemeba , Saccamoeba .
      - Familia Nolandellidae Cavalier-Smith 2011, Lahr & Katz 2011 , género Nolandella .
    - Orden Arcellinida Kent 1880 . Géneros incertae sedis : Acipyxis , Apolimia , Argynnia , Armipyxis , Conicocassis , Cornuapyxis , Ellipsopyxella , Ellipsopyxis , Erugomicula , Frenopyxis , Geamphorella , Geoplagiopyxis , Geopyxella , Hoogenraadia , Jungia , Lagenodifflugia , Lamptopyxis , Lamtoquadrula , Leptochlamys , Maghrebia , Meisterfeldia , Microquadrula , Nabranella , Oopyxis , Paracentropyxis , Paraquadrula , Pentagonia , Physochila , Planhoogenraadia , Pomoriella , Pontigulasia , Prantlitina , ^{[ 33 ]} Proplagiopíxis , Protoplagiopíxis , Protocucurbitella , Pseudawerintzewia , Pseudonebela , Schoenbornia , Sexangularia , Suiadifflugia , Trigonopyxis , Wailesella , ^{[ 29 ]} † Cangwuella . ^{[ 34 ]}
      - Suborden Phryganellina Bovee 1985
        Familia Phryganellidae Jung 1942 , género Phryganella .
        Familia Cryptodifflugiidae Jung 1942 , género Cryptodifflugia . ^{[ 35 ]}
      - Suborden Organoconcha Lahr et al. 2019 , familia Microchlamyiidae Ogden 1985 , géneros Microchlamys (= Pseudochlamys ), Spumochlamys , Pyxidicula .
      - Suborden Glutinoconcha Lahr et al. 2019
        Infraorden Volnustoma Lahr et al. 2019 , familia Heleoperidae Jung 1942 , géneros Heleopera , Metaheleopera .
        Infraorden Hyalospheniformes Lahr et al. 2019 , familia Hyalospheniidae Schulze 1877 enmienda. Kosakyan & Lara 2012 (=Nebelidae Taranek 1882 ), géneros Arabasta , Alocodera , Apodera , Certesella , Cornutheca , Gibbocarina , Hyalosphenia , Longinebela , Mrabella , Nebela , Padaungiella , Planocarina , Porosia , Quadrulella .
        Infraorden Excentrostoma Lahr et al. 2019 , familia Centropyxidae Jung 1942 (incl. Plagiopyxidae Bonnet & Thomas 1960 ), géneros Awerinzewia , Bullinularia , Centropyxis , Frenopyxis , ^{[ 36 ]} Golemanskia , Plagiopyxis .
        Infraorden Cylindrothecina González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022 , familia Cylindrifflugiidae González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022 , género Cylindrifflugia .
        Infraorden Longitecina Lahr et al. 2019
        Familia Difflugiidae Wallich 1864 , géneros Difflugia , Zivkovicia .
        Familia Lesquereusiidae Jung 1942 , género Lesquereusia .
        Infraorden Sphaerothecina Kosakyan, Lara & Lahr 2016
        Familia Arcellidae Ehrenberg 1843 , géneros Arcella , Galeripora .
        Familia Netzeliidae Kosakyan et al. 2016 , géneros Cucurbitella , Cyclopyxis , Netzelia .

Clase Discosea Cavalier-Smith et al. 2004 sensu Smirnov et al. 2011
- Subclase Flabellinia Smirnov et al. 2005
  - Superorden Dermelia Jones et al. 2025 ^{[ 37 ]}
    - Orden Mycamoebida Jones & Brown en Jones et al. 2025 , familia Mycamoebidae Jones & Brown en Jones et al. 2025 , géneros Mycamoeba , Janelia , Microglomus .
    - Orden Dermamoebida Cavalier-Smith de 2004 modificada. Kudryavtsev, Voytinsky y Volkova 2022 ^{[ 38 ]}
      - Familia Dermamoebidae Cavalier-Smith & Smirnov 2011 , géneros Dermamoeba , Paradermamoeba , Coronamoeba . ^{[ 38 ]}
      - Familia Mayorellidae Schaeffer 1926 , género Mayorella .
  - Superorden Thecavania Jones et al. 2025 ^{[ 37 ]}
    - Orden Stygamoebida Smirnov & Cavalier-Smith en Smirnov et al. 2011 ^{[ 25 ]}
      - Familia Stygamoebidae Smirnov & Cavalier-Smith en Smirnov et al. 2011 , género Stygamoeba .
      - Familia Vermistellidae Cavalier-Smith en Cavalier-Smith et al. 2016 , género Vermistella . ^{[ 39 ]}
    - Orden Thecamoebida ^{[ d ]} Schaeffer 1926 sensu Smirnov & Cavalier-Smith 2011 , géneros Sappinia , Stenamoeba , Stratorugosa , ^{[ 40 ]} Thecamoeba , Thecochaos . ^{[ 41 ]}
    - Orden Dactylopodida ^{[ d ]} Smirnov et al. 2005 sensu Kang et al. 2017 , géneros Cunea , Janickina , Korotnevella , Neoparamoeba , Paramoeba , Pseudoparamoeba , Vexillifera .
    - Orden Vannellida Smirnov et al. 2005 , familia Vannellidae Bovee 1979 , géneros Clydonella , Lingulamoeba , Paravannella , Pessonella , ^{[ e ]} Ripella , Vannella .
- Subclase Centramoebia Cavalier-Smith et al. 2016
  - Orden Himatismenida ^{[ d ]} Página 1987 , géneros Cochliopodium , Ovalopodium , Parvamoeba .
  - Superorden Acapostellia Gàlvez-Morante, Berney & Richter 2026 ^{[ 42 ]}
    - Orden Acanthopodida ^{[ d ]} Página 1976 (=Centramoebida Rogerson & Patterson 2002 sensu Tice et al. 2016 ), ^{[ 43 ]} géneros Acanthamoeba , Balamuthia , Luapeleamoeba , Protacanthamoeba , Dracoamoeba , Vacuolamoeba .
    - Orden Apostamoebida Gàlvez-Morante, Berney & Richter 2026 , ^{[ 42 ]} familia Apostamoebidae Gàlvez-Morante, Berney & Richter 2026 , género Apostamoeba
    - Orden Pellitida ^{[ d ]} Smirnov & Cavalier-Smith 2011 sensu Kang et al. 2017 , géneros Endostelium , Gocevia , Paragocevia , Pellita .

Evosea Kang et al. 2017
- Clase Cutosea Cavalier-Smith 2016 , orden Squamocutida Cavalier-Smith 2016
  - Familia Squamamoebidae Cavalier-Smith 2016 , géneros Armaparvus , Squamamoeba .
  - Familia Sapocribridae Cavalier-Smith 2016 , género Sapocribrum .
  - Familia Idionecidae Hess & Simpson 2019 , género Idionectes . ^{[ 44 ]}
- Clase Variosea Cavalier-Smith 2004. Géneros no asignados a ningún clado inferior: Angulamoeba , Arboramoeba , Darbyshirella , Dictyamoeba , Ischnamoeba , Heliamoeba , Filamoeba , Phalansterium . ^{[ f ]}
  - Familia Flamellidae Lahr & Katz en Lahr et al. 2011 , géneros Flamella (= Comandonia ), ^{[ 45 ]} Telaepolella Lahr et al. 2012 .
  - Orden Protosteliida (Protosteliales) LSOlive & Stoian. 1966 sensu Shadwick & Spiegel en Adl et al. 2012 , familia Protosteliidae (Protosteliaceae) LSOlive & Stoian. 1966 , género Protostelium (incl. Planoprotostelium ).
  - Orden Fractovitellida Lahr et al. 2011 sensu Kang et al. 2017
    - Familia Acramoebidae Smirnov, Nassonova & Cavalier-Smith 2008 , género Acramoeba .
    - Familia Schizoplasmodiidae Shadwick & Spiegel en Adl et al. 2012 , géneros Ceratiomyxella , Nematostelium , Schizoplasmodium .
    - Familia Soliformoviidae Lahr & Katz 2011 . Géneros: Soliformovum Spiegel 1995 ; Grellamoeba Dyková, Kostka y Pecková 2008 .
  - Orden Cavosteliida (Cavosteliales) Shadwick & Spiegel en Adl et al. 2012 , familia Cavosteliidae (Cavosteliaceae) Olive & Stoianovitch 1964 , géneros Cavostelium , Schizoplasmodiopsis , Tychosporium .
  - Orden Holomastigida Lauterborn 1895 (incl. Artodiscida Cavalier-Smith 2013 ), familia Multiciliidae Poche 1913 (incl. Artodiscidae Cavalier-Smith 2013 ), géneros Artodiscus , Multicilia .
- Clase Archamoebea Cavalier-Smith 1983 sensu Pánek et al. 2016 ^{[ 46 ]}
  - Familia Tricholimacidae Cavalier-Smith 2012 , género Tricholimax .
  - Orden Entamoebida Cavalier-Smith 1993 , familia Entamoebidae Chatton 1925 , géneros Entamoeba , † Entamoebites . ^{[ 47 ]}
  - Orden Pelobiontida Página 1976 sensu Pánek et al. 2016
    - Suborden Pelomyxina Starobogatov 1980 estadística. nov. Panek et al. 2016 , familia Pelomyxidae Schulze 1877 , géneros Mastigella (= Mastigamoeba ), Pelomyxa .
    - Suborden Mastigamoebina Frenzel 1897 estadística. nov. Panek et al. 2016
      - Familia Rhizomastixidae Ptáčková et al. 2013 , género Rhizomastix .
      - Familia Mastigamoebidae Goldschmidt 1907 , géneros Endamoeba , Endolimax , Iodamoeba , Mastigamoeba , Mastigina .
- Eumycetozoa Zopf 1884 sensu Kang et al. 2017 (=Mycetozoa de Bary 1859 ex Rostafinski 1873 , Macromycetozoa Fiore-Donno 2010 )
  - Clase Dictyostelea Lister 1909 sensu Sheikh et al. 2018 (Dictyosteliomycetes Doweld 2001 ). Género no asignado a ningún orden: Synstelium . Género incertae sedis : Coenonia . ^{[ 48 ]}
    - Orden Acytosteliales S.Baldauf S.Sheikh & Thulin 2018
      - Familia Acytosteliaceae Raper ex Raper & Quinlan 1958 , géneros Acytostelium , Rostrostelium , Heterostelium .
      - Familia Cavenderiaceae S.Baldauf, S.Sheikh & Thulin 2018 , género Cavenderia .
    - Orden Dictyosteliales L.S.Olive ex PMKirk et al. 2001 . Género no asignado a ninguna familia: Coremiostelium .
      - Familia Dictyosteliaceae Rostaf. ex Cooke 1877 , géneros Dictyostelium , Polysphondylium .
      - Familia Raperosteliaceae S.Baldauf S.Sheikh & Thulin 2018 , géneros Hagiwaraea , Raperostelium , Speleostelium , Tieghemostelium .
  - Clase Ceratiomyxomycetes (Ceratiomyxea) D. Hawksw., B. Sutton & Ainsw. 2019 , ^{[ 28 ]} orden Protosporangiida Shadwick & Spiegel en Adl et al. 2012 (Ceratiomyxales GW Martin ex ML Farr & Alexop. )
    - Familia Ceratiomyxaceae (Ceratiomyxidae) J.Schröt. 1889 , género Ceratiomyxa .
    - Familia Protosporangiidae Spiegel en Adl et al. 2012 (Protosporangiaceae Leontyev, Stephenson, Schnittler, Shchepin & Novozhilov 2020 ), géneros Clastostelium , Protosporangium . ^{[ 13 ]}
  - Clase Myxogastrea Cavalier-Smith 1993 (Myxomycetes G.Winter 1880 ) (=Myxogastres Fr. 1829 , Myxogasteres Schröt., 1889 , Endosporeae Rostaf. 1873 , Myxogastromycetidae GWMartin 1961 , Myxogastromycetes M.Locquin 1974 , Myxogastria Cavalier-Smith 2012 como "Myxogastria LSOlive 1970" nom. inval. ) ^{[ 28 ]}
    - Subclase Lucisporinia Cavalier-Smith 2013 como "Lucisporidia" (Lucisporomycetidae Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 ). Géneros incertae sedis : Arcyriatella , Calonema , Minakatella , Trichioides .
      - Superorden Cribariidia Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , orden Cribariales (Cribariida) T.Macbr. 1922 , familia Cribariaceae (Cribariidae) Corda 1838 , géneros Cribaria , Lindbladia , Licaethalium .
      - Superorden Trichiidia Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019
        Orden Reticulariales (Reticulariida) Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , familia Reticulariaceae (Reticulariidae) Chevall. ex Corda 1842 , géneros: Alwisia , Lycogala , Reticularia , Tubifera .
        Orden Liceales (Liceida), familia Liceaceae (Liceidae) Chevall. 1826 , géneros Licea , Listerella .
        Orden Trichiales (Trichiida) T.Macbr. 1922
        Familia Dianemataceae (Dianematidae) T.Macbr. 1922 , géneros Calomyxa , Dianema , Dictydiaethalium , Prototrichia .
        Familia Trichiaceae (Trichiidae) Chevall. 1826 sensu Martin & Alexopoulos 1969 , géneros Hemitrichia (incluido Trichia decipiens ), Arcyria (incluido Arcyodes ); Perichaena^(P) , Trichia (incl. Cornuvia , Metatrichia , Oligonema ).
    - Subclase Columellinia Cavalier-Smith 2013 como "Columellidia" (Columellomycetidae Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 ) (=Fuscisporidia Cavalier-Smith 2013 sensu Kretzschmar et al. 2015 ). Géneros incertae sedis : Diachea , Echinosteliopsis , Leptoderma , Paradiachea , Protophysarum , Trabrooksia , Willkommlangea .
      - Superorden Echinosteliidia Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , orden Echinosteliales (Echinosteliida) GW Martin 1961 , familia Echinosteliaceae (Echinosteliidae) Rostaf. ex Cooke 1877 , géneros: Barbeyella , Echinostelium (incl. Semimorula ).
      - Superorden Stemonitidia Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019
        Orden Clastodermatales (Clastodermatida) Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , familia Clastodermataceae (Clastodermatidae) Alexop. & TE Brooks 1971 , género Clastoderma .
        Orden Meridermatales (Meridermatida) Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , familia Meridermataceae (Meridermatidae) Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , género Meriderma .
        Orden Stemonitales (Stemonitida) T.Macbr. Enmienda de 1922 . Leontyev, Schnittler, SLStephenson, Novozhilov y Shchepin 2019
        Familia Stemonitidaceae (Stemonitidae) Fr. 1829 emend. Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , géneros Macbrideola , Stemonitis , Symphytocarpus .
        Familia Amaurochaetaceae (Amaurochaetidae) Rostaf. ex Cooke 1877 emend. Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , géneros Comatricha , Stemonaria , Stemonitopsis , Amaurochaete , Brefeldia , Enerthenema , Paradiacheopsis .
        Orden Physarales (Physarida) T.Macbr. 1922. Género no asignado a ninguna familia: Tasmaniomyxa . ^{[ 49 ]}
        Familia Lamprodermataceae (Lamprodermatidae) T.Macbr. Enmienda de 1899 . Leontyev, Schnittler, SLStephenson, Novozhilov & Shchepin 2019 , géneros Lamproderma (incl. Dichaeopsis , Colloderma , Elaeomyxa ), Collaria^(P) .
        Familia Didymiaceae (Didymiidae) Rostaf. ex Cooke 1877 , géneros Diderma , Didymium , Lepidoderma , Mucilago .
        Familia Physaraceae (Physaridae) Chevall. 1826 , géneros Craterium , Leocarpus , Fuligo , Physarum (incl. Badhamia ), Physarella , Physarina , Kelleromyxa .

Arqueoplastos

Filo Glaucophyta Skuja 1954 (=Glaucocystaceae West 1904 , Glaucocystophyta Kies y Kremer 1986 , Glaucoplantae Marin & Melkonian en Li et al. 2020 ). Incertae sedis géneros: Archaeopsis , Chalarodora , Glaucocystopsis , Peliaina , Strobilomonas . ^{[ 50 ]}
- Orden Cyanophorales Kies & Kremer 2006 . Único género: Cyanophora .
- Orden Glaucocystales Bessey 1907 . Único género: Glaucocystis .
- Orden Gloeochaetales Bessey 1907 . Géneros: Cyanoptyche , Gloeochaete .
Filo Picozoa Seenivasan, Sausen, Medlin & Melkonian 2013 (=picobiliphytes Not et al. 2007 ) → clase Picomonadea Seenivasan, Sausen, Medlin & Melkonian 2013 → orden Picomonadida Seenivasan, Sausen, Medlin & Melkonian 2013 → familia Picomonadidae Seenivasan, Sausen, Medlin & Melkonian 2013 . Género único: Picomonas Seenivasan, Sausen, Medlin & Melkonian 2013 . ^{[ g ]}
Filo Rhodelphidea Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → clase Rhodelphidea Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → orden Rhodelphida Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → familia Rhodelphidae Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 . Género único: Rhodelphis Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 . ^{[ 52 ]}
Filo Rhodophyta Wettstein 1901 (=Rhodophyceae Thuret 1855, enmienda. Rabenhorst 1863 , Rhodoplantae Saunders y Hommersand 2004 enmienda. Adl et al. 2005 )

Cloroplastida

Filo Prasinodermophyta Marin y Melkonian en Li et al. 2020 ^{[ 53 ]}
- Clase Prasinodermophyceae Marin & Melkonian en Li et al. 2020 → pedir Prasinodermatales Marin & Melkonian en Li et al. 2020 → familia Prasinodermataceae Marin & Melkonian en Li et al. 2020 . Género único: Prasinoderma Hasegawa & Chihara en Hasegawa et al. 1996 .
- Clase Palmophyllophyceae Leliaert et al. Enmienda de 2016. Marin y Melkonian en Li et al. 2020
  - Orden Palmophyllales Zechman, Verbruggen, Leliaert, Ashwort, MABuchheim, Fawley, H.Spalding, Pueschel, JABuschheim, Verghese & Hanisak 2010 → familia Palmophyllaceae Zechman, Verbruggen, Leliaert, Ashwort, MABuchheim, Fawley, H.Spalding, Pueschel, JABuschheim, Verghese & Hanisak 2010 . Géneros: Palmophyllum Kützing 1849 ; Verdigellas Ballantine & Norris 1994 ; Palmoclathrus Womersley 1971 . ^{[ 54 ]}
  - Orden Prasinococcales Guillou et al. ex Leliaert et al. Enmienda de 2016. Marin y Melkonian en Li et al. 2020 → familia Prasinococcaceae Leliaert et al. 2016 . Género único: Prasinococcus Miyashita & Chihara en Miyashita et al. 1993 .
Phylum Chlorophyta Reichenbach 1828 enmienda. Pascher enmienda de 1914. Lewis y McCourt 2004
- Clase Chloropicophyceae Lopes dos Santos & Eikrem 2017 → orden Chloropicales Lopes dos Santos & Eikrem 2017 → familia Chloropicaceae Lopes dos Santos & Eikrem 2017 . Géneros: Cloroparvula Lopes dos Santos & Eikrem 2017 ; Cloropicon Lopes dos Santos & Eikrem 2017 .
- Clase Mamiellophyceae Marin & Melkonian 2010
  - Orden Mamiellales Moestrup de 1984 modificada. Marín y Melkonian 2010
    - Familia Bathycoccaceae Marin & Melkonian 2010 . Géneros: Bathycoccus Eikrem y Throndsen 1990 ; Ostreococcus Courties y Chrétiennot-Dinet 1995 .
    - Familia Mamiellaceae Moestrup 1984 enmienda. Marín y Melkonian 2010 . Géneros: Mamiella Moestrup 1984 ; Mantoniella Desikachary 1972 ; Micromonas Manton y Parke 1960 .
  - Pedido Dolichomastigales Marin & Melkonian 2010
    - Familia Crustomastigaceae Marin & Melkonian 2010 . Género único: Crustomastix Nakayama, Kawachi & Inouye 2000 .
    - Familia Dolichomastigaceae Marin & Melkonian 2010 . Género único: Dolichomastix Manton 1977 .
  - Orden Monomastigales R.E.Norris ex Marin & Melkonian 2010 (=Monomastigales Norris en Parker 1982 nomen nudum ) → familia Monomastigaceae Marin & Melkonian 2010. Único género: Monomastix Scherffel 1912 .
- Clase Nephroselmidophyceae Cavalier-Smith 1993 emend. Yamaguchi 2011 → orden Nephroselmidales Nakayama, Suda, Kawachi & Inouye 2007 → familia Nephroselmidaceae Pascher 1913 ex Silva 1980 . Género: Nephroselmis Stein 1878 .
- Clase Picocystophyceae Lopes dos Santos & Eikrem 2017 → orden Picocystales Lopes dos Santos & Eikrem 2017 → familia Picocystaceae Lopes dos Santos & Eikrem 2017 . Género único: Picocystis R.A.Lewin en Lewin et al. 2000 .
- Clase Pseudoscourfieldiophyceae Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 → orden Pseudoscourfieldiales Melkonian 1990 ex Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 → familia Pseudoscourfieldiaceae Melkonian 1990 ex Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 (=Pycnococcaceae Guillard en Guillard, Keller, O'Kelly & Floyd 1991 enmienda. MWFawley en Fawley et al. 1999. Género único: Pseudoscourfieldia Manton 1975 (= Pycnococcus Guillard ^en^{Guillard ,} Keller, O'Kelly & Floyd 1991 ). ^]
- Clase Pyramimonadophyceae Moestrup & Daugbjerg en Daugbjerg et al. 2020 ^{[ 56 ]} → pedir Pyramimonadales Chadefaud 1950
  - Familia Pyramimonadaceae Korshikov 1938. Géneros: Cymbomonas Schiller 1913 ; Pyramimonas Schmarda 1850 ; " Prasinopapilla " (no descrito formalmente).
  - Familia Halosphaeraceae Haeckel 1894 . Géneros: Halosphaera Schmitz 1878 ; Pachysphaera Ostenfeld 1899 ; † Tasmanites E.Newton 1875 .
- Clorofitas centrales
  - Clase Chlorodendrophyceae Massjuk 2006 → orden Chlorodendrales Berger 1954 como "Chlorodendrinales" (=Tetraselmidales Ettl. 1982 ) → familia Chlorodendraceae Oltmanns 1904 . Géneros: Prasinocladus Kuckuck 1894 ; Scherffelia Pascher 1912 ; Tetraselmis Stein 1878 .
  - Clase Pedinophyceae Moestrup 1991 enmienda. Fawley, Zechman y Buchheim en Adl et al. 2012 ^{[ 57 ]}
    - Pedido Marsupiomonadales Marin 2012
      - Familia Marsupiomonadaceae Marin 2012 . Género único: Marsupiomonas Jones, Leadbeater & Green 1994 .
      - Familia Resultomonadaceae Marin 2012. Único género: Resultomonas Marin 2012 .
    - Orden Pedinomonadales Moestrup de 1991 modificada. Marin 2012 → familia Pedinomonadaceae Korshikov 1938 . Géneros: Clorochytridion Vischer 1945 ; Pedinomonas Korshikov 1923 .
  - clado UTC
    - Clase Chlorophyceae Wille 1884
      - Clado SV ^{[ 58 ]}
        Orden Sphaeropleales ^(P?)Luerssen 1877 . Géneros Incertae sedis: Spermatozopsis Korshikov 1913 ; Golenkinia Chodat 1894 ; Jenufa Němcová, M. Eliáš, Škaloud y Neustupa 2011 ; Johansenicoccus . ^{[ 59 ]}^{[ 58 ]}^{[ 60 ]}
        Familia Dictyochloridaceae Fučíková, POLewis & LALewis 2013 . Género único: Dictyochloris Vischer 1945 .
        Familia Sphaeropleaceae Kützing 1849
        Familia Microsporaceae Bohlin 1901
        Treubarinia . Géneros: Trochiscia Kützing 1834 ; Treubaria C.Bernard 1908 ; Cylindrocapsa Reinsch 1867 ; Elakatothrix Wille 1898 . ^{[ 58 ]}
        Scenedesminia ("tradicional" Sphaeropleales) ^{[ 58 ]}
        Familia Bracteacoccaceae P.M.Tsarenko 2005 . Género único: Bracteacoccus Tereg 1922 .
        Familia Bracteamorphaceae Fučíková, POLewis & LALewis 2013 . Género único: Bracteamorpha Fučíková, POLewis & LALewis 2013 .
        Familia Chromochloridaceae Fučíková, POLewis & LALewis 2013 . Género único: Chromochloris Kol & Chodat 1934 .
        Familia Dictyococcaceae Fučíková, POLewis & LALewis 2013 . Género único: Dictyococcus Gerneck 1907 .
        Familia Hydrodictyaceae Dumortier 1829. Géneros: Hydrodictyon Roth ; Lacunastrum H.A.McManus ; Monactinus Corda ; Parapediastrum^(P)E.Hegewald ; Pediastrum Meyen . ^{[ 61 ]}
        Familia Mychonastaceae Fučíková, POLewis & LALewis 2013 . Género único: Mychonastes P.D.Simpson & SDVan Valkenburg 1978 .
        Familia Neochloridaceae Ettl & Komárek 1982
        Familia Pseudomurielaceae Fučíková, POLewis & LALewis 2013 . Género único: Pseudomuriella N.Hanagata 1998 .
        Familia Scenedesmaceae Oltmanns 1904
        Familia Schizochlamydaceae Fučíková, POLewis & LALewis 2013 . Género único: Schizochlamys Braun ex Kützing 1849 .
        Familia Selenastraceae Blackman & Tansley 1903 (=Ankistrodesmaceae Korshikov 1953 )
        Familia Radiococcaceae
        Familia Rotundellaceae Fučíková, POLewis & LALewis 2013 . Género único: Rotundella Fučíková, POLewis & LALewis 2013 .
        Familia Tumidellaceae Fučíková, POLewis & LALewis 2013 . Género único: Tumidella Fučíková, POLewis & LALewis 2013 .
        Pedido Volvocales Poche 1913
      - Clado OCC ^{[ 58 ]}^{[ 60 ]}
        Orden Chaetopeltidales O'Kelly, Watanabe & Floyd
        Orden Chaetophorales Wille 1901
        Orden Oedogoniales Heering 1914
    - Clase Trebouxiophyceae Friedl 1995 (=Pleurastrophyceae Mattox et al. 1984 )
    - Clase Ulvophyceae ^(P)
Phylum Streptophyta Bremer & Wanntorp 1981 (= Charophyta Migula 1897 enmienda. Karol et al. 2009 )
- Clase Chlorokybophyceae Irisarri et al. 2021 → ordenar Chlorokybales Irisarri et al. 2021 → familia Chlorokybaceae Irisarri et al. 2021 . Género único: Chlorokybus Geitler 1942 . ^{[ 62 ]}
- Clase Mesostigmatophyceae Marin & Melkonian 1999 enmienda. Lewis & McCourt 2004 (=Mesostigmata Turmel et al. 2002 ) → orden Mesostigmales Cavalier-Smith 1998 → familia Mesostigmataceae Fott 1947 . Único género: Mesostigma Lauterborn 1894 .
- Clase Klebsormidiophyceae C. Jeffrey ex Guiry 2023 ^{[ 63 ]}
  - Orden Klebsormidiales Bierenbroodspot et al. 2024 → familia Klebsormidiaceae Bierenbroodspot et al. 2024 . Géneros: Klebsormidium Silva, Mattox y Blackwell 1972 ; Interfilum Chodat 1992 ; Streptofilum Mikhailyuk y Lukešová 2018 .
  - Orden Entransiales Bierenbroodspot et al. 2024 → familia Entransiaceae Bierenbroodspot et al. 2024 . Género único: Entransia E.O. Hughes 1948 .
  - Orden Hormidiellales Bierenbroodspot et al. 2024 → familia Hormidiellaceae Bierenbroodspot et al. 2024 . Géneros: Hormidiella Iyengar y Kanthamma 1940 ; Streptosarcina Mikhailyuk & Lukešová 2018 .
- Phragmoplastophyta Lecointre y Guyander 2006
  - Clase Charophyceae Smith enmienda de 1938. Karol et al. 2009
  - Clase Coleochaetophyceae Jeffrey 1982
  - Anydrophyta Rensing 2020 ^{[ 64 ]}
    - Clase Zygnematophyceae van den Hoek et al. Enmienda de 1995. Hall y cols. 2009 ^{[ 65 ]}
      - Orden Serritaeniales S.Hess & J.de Vries 2022 → familia Serritaeniaceae S.Hess & J.de Vries 2022 . Género único: Serritaenia A.Busch & S.Hess 2021 .
      - Orden Zygnematales Bessey 1907 enmienda. Hess & de Vries 2022 → familia Zygnemataceae Kützing 1843 . Géneros: Cylindrocystis Meneghini 1848 ; Mesotaenium Nägeli 1849 ; Mougeotia (Roth) C.Agardh 1824 ; Zygnema C.Agardh 1817 nom. contras. ; Zygnemopsis (Skuja) Transeau 1934 .
      - Orden Desmidiales Bessey 1907 emend. S.Hess & J.de Vries 2022 → familia Desmidiaceae Ralfs 1848 . Géneros: Bambusina Kützing ex Kützing 1849 nom. cons. ; Closterium Nitzsch ex Ralfs 1848 ; Cosmarium Corda ex Ralfs 1848 ; Cosmocladium Brébisson 1856 ; Desmidium C.Agardh ex Ralfs 1848 ; Euastrum Ehrenberg ex Ralfs 1848 ; Micrasterias C.Agardh ex Ralfs 1848 ; Netrium (Nägeli) Itzigsohn & Rothe 1856 ; Nucleotaenium Gontcharov & Melkonian 2010 ; Onychonema G.C.Wallich 1860 ; Penium Brébisson ex Ralfs 1848 ; Phymatodocis Nordstedt 1878 ; Planotaenium (Ohtani) Petlovany & Palamar-Mordvintseva 2009 ; Pleurotaenium Nägeli 1849 ; Staurastrum Meyen ex Ralfs 1848 ; Staurodesmus Teiling 1948 ; Xanthidium Ehrenberg ex Ralfs 1848 ; etc.
      - Orden Spirogyrales Clements nom. contras. enmendar. Hess y de Vries 2022 . Único género: Spirogyra Link 1820 nom. contras.
    - Embryophyta Engler 1886 emend. Lewis & McCourt 2004 (=Plantae Haeckel 1866 ). Excluido de los protistas.

Pancryptista

El filo Cryptista contiene flagelados unicelulares heterótrofos y fotosintéticos. Su clasificación ha sufrido muchos cambios a lo largo de los años, y coexisten varios sistemas y nomenclaturas conflictivos. Fue descrito por Thomas Cavalier-Smith en 1989 para unir dos grupos distintos de flagelados: las criptomónadas fotosintéticas y las goniomónadas heterótrofas (respectivamente las dos clases Cryptomonadea y Cyathomonadea). El nombre Cryptista pretendía ser un sinónimo de Cryptophyta, ^{[ 68 ]} el filo de algas descrito por el mismo autor en años anteriores. ^{[ 69 ]} En 2004, modificó la clasificación de Cryptista para añadir dos subfilos: Cryptomonada, que contiene las clases mencionadas anteriormente (renombradas como Cryptophyceae y Goniomonadea respectivamente), y Leucocrypta, que contiene los katablepharids heterótrofos . ^{[ 70 ]} Al año siguiente, un grupo separado de autores propuso una clasificación superior diferente para los katablepharids como un filo Kathablepharida o Filo Katablepharidophyta, relacionado con pero independiente del filo Cryptophyta, sin mencionar a Cryptista. ^{[ 71 ]} Entre 2013 y 2015, Cavalier-Smith actualizó la clasificación una vez más al describir tres nuevos subfilos: Rollomonadia, que contiene los subfilos anteriores reducidos a superclases; Palpitia, que contiene el flagelado Palpitomonas bilix ; ^{[ 72 ]} y Corbihelia, que contiene picozoos , telonémidos y algunas especies de heliozoos ( Heliomorpha y Microheliella ). ^{[ 73 ]} Corbihelia no llegó a un consenso: análisis y revisiones posteriores separaron a los telonémidos y picozoos como sus propios clados, y colocaron a Heliomorpha en Cercozoa . ^{[ 10 ]} Sin embargo, la adición de Palpitomonas y la monofilia de Rollomonadia han sido respaldadas en otros análisis. ^{[ 66 ]}

Cryptista fue redefinido en la revisión ISOP de 2019 como el clado que contiene Palpitomonas , katablepharids, goniomonads y cryptomonads. Sin embargo, esta revisión introdujo otro sistema de clasificación que es contradictorio con los anteriores. Propusieron una sola clase Cryptophyceae que unía cryptomonads, goniomonads y katablepharids, y trataron a cryptomonads como un solo orden Cryptomonadales, ^{[ 10 ]} aunque esto no sigue el consenso científico: hay más órdenes de cryptomonads (por ejemplo, Pyrenomonadales , Tetragonidiales ) y el nombre Cryptophyceae ya se usaba para taxones que excluían a katablepharids ^{[ 74 ]} y a menudo también excluían a goniomonads. ^{[ 73 ]} No ha habido una nueva revisión desde entonces.

A diferencia de Heliomorpha , el género Microheliella fue secuenciado genéticamente y sus afinidades se han resuelto. En 2022, se propuso como el grupo hermano de Cryptista, en un clado conocido como Pancryptista . ^{[ 67 ]}

Pancriptista Yazaki et al. 2022

Orden Microhelida Cavalier-Smith & Chao 2012 , familia Microheliellidae Cavalier-Smith & Chao 2012 , género Microheliella .
Phylum Cryptista Cavalier-Smith enmienda de 1989. Adl et al. 2019
- Subfilo Palpitia Cavalier-Smith & Chao 2012 , clase Palpitea Cavalier-Smith & Chao 2012 , orden Palpitida Cavalier-Smith & Chao 2012 , familia Palpitomonadidae Cavalier-Smith & Chao 2012 , género Palpitomonas .
- Subfilo Rollomonadia Cavalier-Smith 2013 (=Cryptophyta Silva 1962 ; Cryptophyta Cavalier-Smith 1986 ; Cryptophyceae Pascher 1913 enmienda. Schoenichen 1925 enmienda. Adl et al. 2012 )
  - Superclase Leucocrypta Cavalier-Smith 2004 stat. nov. 2013 (="filo" Kathablepharida (Katablepharidophyta) Okamoto & Inouye 2005 ), clase Leucocryptea Cavalier-Smith 2004 (=Kathablepharidea (Katablepharidophyceae) Okamoto & Inouye 2005 ), orden Kathablepharidida (Katablepharidales) Okamoto & Inouye 2005 , familia " Kathablepharididae " Vørs 1992 emend. Clay & Kugrens 1999 (Katablepharidaceae Skuja 1939 ), géneros Hatena , Kathablepharis , Leucocryptos , Platychilomonas , Roombia .
  - Superclase Cryptomonada Cavalier-Smith 2004
    - Clase Goniomonadea Cavalier-Smith 1993 (=Cyathomonadea Cavalier-Smith 1989 ) ^{[ h ]}
      - Orden Goniomonadida (Goniomonadales) Novarino & Lucas 1993 (=Cyathomonadales Lee 1989 ), géneros Aquagoniomonas , Baltigoniomonas , Cosmogoniomonas , Limnogoniomonas , Marigoniomonas , Naiadagoniomonas , ^{[ 75 ]} Neptunogoniomonas , Poseidogoniomonas , Thalassogoniomonas . ^{[ 76 ]}
        Familia Goniomonadidae (Goniomonadaceae) Hill 1991 (=Cyathomonadaceae Pringsheim 1944 ), género Goniomonas (= Cyathomonas ). ^{[ 77 ]}
      - Orden Hemiarmida Cavalier-Smith 2018 , familia Hemiarmidae Cavalier-Smith 2018 , género Hemiarma . ^{[ 77 ]}
    - Clase Cryptophyceae Fritsch en West & Fritsch 1927 ( Cryptomonadea Stein 1878 stat. nov. Pascher ex Schoenichen 1925 ). Genera incertae sedis : Bjornbergiella , ^{[ 74 ]} Cyanomonas , Plagioselmis . ^{[ 78 ]}
      - Orden Cryptomonadales Pascher 1913 enmienda. Arcilla y col. 1999
        Familia Baffinellaceae Daugbjerg & Norlin 2018 , género Baffinella . ^{[ 79 ]}
        Familia Cryptomonadaceae Clay et al. 1999 , géneros Cryptomonas , Chilomonas .
      - Orden Pyrenomonadales Clay et al. 1999
        Familia Pyrenomonadaceae Novarino & Lucas 1993 , géneros Pyrenomonas (= Rhodomonas ), Storeatula , Rhinomonas .
        Familia Geminigeraceae Clay et al. 1999 , géneros Geminigera , Teleaulax , Hanusia , Guillardia , Proteomonas .
        Familia Chroomonadaceae Clay et al. 1999 , géneros Chroomonas , Falcomonas , Komma .
        Familia Hemiselmidaceae Butcher 1967 , género Hemiselmis .
      - Orden Tetragonidiales Kristiansen 1992 , familia Tetragonidiaceae Bourrelly ex Silva 1980 , género Tetragonidium . ^{[ i ]}

Haptista

Haptophyta Hibberd 1976 ex. Edvardsen y Eikrem 2000
- Pavlovales Green 1976 [Pavlovophyceae Cavalier-Smith 1986 ]. Diacronema , Exanthemachrysis , Pavlova , Rebecca .
- Prymnesiophyceae Hibberd 1976
  - Prymnesiales Papenfuss 1955, enmienda. Edvardsen y Eikrem 2000 . Crisocromulina , Crisocampanula , Dicrateria , Haptolina , Prymnesium , Pseudohaptolina .
  - Phaeocystales Medlin 2000 . Phaeocystis .
  - Isochrysidales Pascher 1910, enmienda. Edvardsen y Eikrem 2000 . Emiliania , Gephyrocapsa , Isochrysis , Ruttnera , Tisochrysis .
  - Coccolithales Schwarz 1932, enmienda. Edvardsen y Eikrem 2000 . Balaniger , Calciosolenia , Coccolithus , Hymenomonas , Chrysotila , Wigwamma .
- Rappephyceae M. Kawachi, R. Kamikawa y T. Nakayama 2021 ^{[ 80 ]}
  - Pavlomulinales M. Kawachi & I. Inouye 2021 . Pavlomulina .
Clase Centroplasthelida Febvre-Chevalier & Febvre 1984 (=Centrohelea Kühn 1926 sensu Cavalier-Smith en Yabuki et al. 2012 ; Centroheliozoa Dürrschmidt & Patterson 1987 ). ^{[ 81 ]} Genera incertae sedis : Meringosphaera , ^{[ 82 ]} Parasphaerastrum .
- Familia Spiculophryidae Shɨshkin & Zlatogursky 2018 , género Spiculophrys .
- Superorden Pterocystida Cavalier-Smith y von der Heyden 2007, enmienda. Shɨshkin y Zlatogursky 2018
  - Orden de Raphidista Shɨshkin y Zlatogursky 2018
    - Familia Choanocystidae Cavalier-Smith & von der Heyden 2007 , género Choanocystis .
    - Familia Raphidiophryidae Febvre-Chevalier & Febvre 1984, enmienda. Shɨshkin y Zlatogursky 2018 , género Raphidiophrys .
  - Orden Pterista Shɨshkin y Zlatogursky 2018
    - Familia Oxnerellidae Cavalier-Smith & Chao 2012 , género Oxnerella .
    - Familia Pterocystidae Cavalier-Smith & von der Heyden 2007 , géneros Pterocystis , Raineriophrys , Chlamydaster , Pseudoraphidiophrys , Pseudoraphidocystis , Triangulopteris , ^{[ 83 ]} Khitsovia . ^{[ 84 ]}
    - Familia Heterophryidae Poche 1913, enmienda. Cavalier-Smith & von der Heyden 2007 , géneros Heterophrys , Sphaerastrum .
    - Familia Clypiferidae Shɨshkin en Shɨshkin et al. 2021 , género Clypifer . ^{[ 81 ]}
- Superorden Panacanthocystida Shɨshkin & Zlatogursky 2018
  - Orden Chthonida Shɨshkin & Zlatogursky 2018 , suborden Yogsothothina Shɨshkin & Zlatogursky 2018 , familia Yogsothothidae Shɨshkin & Zlatogursky 2018 , géneros Yogsothoth , Pinjata . ^{[ 85 ]}
  - Orden Acanthocystida Cavalier-Smith & von der Heyden, enmienda de 2007. Shɨshkin y Zlatogursky 2018
    - Suborden Marophryina Cavalier-Smith en Yabuki et al. 2012 , familia Marophryidae Cavalier-Smith & von der Heyden 2007 emend. Shɨshkin & Zlatogursky 2018 , género Marophrys .
    - Suborden Chalarothoracina Hertwig & Lesser 1874 sensu Cavalier-Smith en Yabuki et al. Enmienda de 2012. Shɨshkin y Zlatogursky 2018
      - Familia Acanthocystidae Claus 1874 emend. Shɨshkin & Zlatogursky 2018 , género Acanthocystis .
      - Familia Raphidocystidae Zlatogursky 2018 , género Raphidocystis .

Estramenópilos

Clase Platysulcea Cavalier-Smith 2018 → orden Platysulcida Cavalier-Smith 2018 → familia Platysulcidae Shiratori, Nakayama & Ishida 2015 . Único género: Platysulcus Shiratori, Nakayama & Ishida 2015 .

Bigira

Bigyra se propuso inicialmente como un filo de protistas heterótrofos estrechamente relacionados con los heterocontos fotosintéticos ( Ochrophyta ). Contenía tres subfilos: Pseudofungi (oomicetos e hifocítridos), Bigyromonada (biflagelados de vida libre) y Opalinata (grandes simbiontes intestinales multiflagelados). El filo se propuso con una característica unificadora: la presencia de una zona de transición flagelar con doble hélice o anillos. Esta definición se modificó posteriormente para excluir tanto a Pseudofungi como a Bigyromonada, y se redujo a dos subfilos diferentes: Opalozoa (que incluye Opalinata y bicosoécidos ) y Sagenista . Antes de esto, Sagenista también era un filo que contenía bicosoécidos y laberíntulos , pero se redujo a solo laberíntulos y algunos flagelados. ^{[ 86 ]}^{[ 77 ]}

La definición actual de Bigyra es parafilética según algunos análisis filogenéticos, con Sagenista más estrechamente relacionado con Gyrista. A pesar de su probable parafilia, la mayoría de los taxónomos continúan usándola, y fue reconocida en la revisión de 2019 por la ISOP, que prioriza los taxones monofiléticos. ^{[ 10 ]}^{[ 87 ]} Su clasificación global fue revisada por última vez por Cavalier-Smith en 2013 y 2018, ^{[ 88 ]}^{[ 77 ]} mientras que la clase específica Placididea fue revisada en 2021, con nuevos taxones descritos por Alexandra Rybarski y coautores, ^{[ 89 ]} y las clases Labyrinthulea y Opalinea fueron revisadas en profundidad en el Handbook of the protists de 2017. ^{[ 90 ]}^{[ 91 ]}

Phylum Bigyra ^(P?)Cavalier-Smith 1998 enmienda. 2013

Subfilo Opalozoa Cavalier Smith, enmienda de 1991. 2006
- Infrafilo Placidozoa Cavalier-Smith 2013
  - Superclase Wobblata ^(P)Cavalier-Smith en Cavalier-Smith y Chao, 2006 stat. n. 2013
    - Clase Placididea Moriya, Nakayama & Inouye 2002 , orden Placidida Moriya, Nakayama & Inouye 2002 , familia Placididae Moriya, Nakayama & Inouye 2002 , géneros Allegra , Haloplacidia , Pendulomonas , Placidia , Placilonga , Suigetsumonas , Wobblia .
    - Clase Nanomonadea Cavalier-Smith en Cavalier-Smith & Scoble 2013 (=clado MAST-3), orden Uniciliatida Cavalier-Smith en Cavalier-Smith & Scoble 2013
      - Familia Incisomonadidae Cavalier-Smith en Cavalier-Smith & Scoble 2013 , género Incisomonas .
      - Familia Solenicolidae Cavalier-Smith en Cavalier-Smith & Scoble 2013 , género Solenicola .
    - Clase Opalomonadea Cavalier-Smith 2013 (=clado MAST-12), sin especies descritas.
  - Superclase Opalinata Wenyon 1926 enmendada por Cavalier-Smith 1997
    - Clase Blastocystea Zierdt et al. 1967 , orden Blastocystida Zierdt 1978 , familia Blastocystidae Jiang & He 1988 , género Blastocystis .
    - Clase Opalinea Wenyon 1926 (=Slopalinida Patterson 1985 )
      - Orden Proteromonadida Grassé 1952 modificada. Cavalier-Smith 1993 , familia Proteromonadidae Grassé 1952 , género Proteromonas (" Prowazekella ").
      - Orden Opalinida Poche 1913 stat. nov. Hall 1953 emend. Cavalier-Smith 2013
        Familia Karotomorphidae Travis 1934 , género Karotomorpha .
        Familia Opalinidae Claus 1874 , géneros Cepedea , Opalina , Protoopalina , Protozelleriella , Zelleriella .
- Infraphylum Bikosia Cavalier-Smith 2018 (=Bicosoecida Grassé 1926 enmienda. Karpov 1998 ), clase Bikosea Cavalier-Smith 1986 como "Bicosoecea" orth. enmendar. 2013 .
  - Familia Pseudobodonidae Cavalier-Smith en Cavalier-Smith & Scoble 2013 , género Pseudobodo .
  - Subclase Bicosidia ^(P?)^{[ 92 ]} Cavalier-Smith en Cavalier-Smith & Chao 2006
    - Superorden Borokiae Cavalier-Smith en Cavalier-Smith & Chao 2006 , orden Borokida (Borokales) Cavalier-Smith en Cavalier-Smith & Chao 2006 , familia Borokidae (Borokaceae) Cavalier-Smith en Cavalier-Smith & Chao 2006 , género Boroka .
    - Superorden Cyathobodoniae ^(P?)^{[ 92 ]} Cavalier-Smith 1993 emend. 2006 . Géneros no asignados a ningún taxón inferior: Halocafeteria , ^{[ 93 ]} Cafileria . ^{[ 94 ]}^{[ 95 ]}
      - Orden Anoecales ^(P?) (Anoecida) Cavalier-Smith 1997 ^{[ j ]} Género no asignado a ningún taxón inferior: Bilabrum. ^{[ 96 ]}
        Familia Anoecaceae Cavalier-Smith en Cavalier-Smith & Chao 2006 , género Anoeca .
        Familia Caecitellaceae (Caecitellidae) Cavalier-Smith en Cavalier-Smith & Chao 2006 , género Caecitellus .
        Familia Cafeteriaceae (Cafeteriidae) Moestrup 1995 , género Cafeteria .
        Familia Symbiomonadaceae Cavalier-Smith en Cavalier-Smith & Chao 2006 , género Symbiomonas .
      - Orden Bicoecida (Bicoecales) Grassé 1926
        Familia Bicosoecidae (Bicosoecaceae) Stein 1878 , géneros Bicosoeca , Stephanocodon , Poteriodendron , Hirugamonas ^{[ 95 ]} .
        Familia Labromonadidae (Labromonadaceae) Cavalier-Smith en Cavalier-Smith & Chao 2006 , género Labromonas .
      - Orden Pseudodendromonadida ("Pseudodendromonadales") Hibberd 1985 emend. Cavalier-Smith 2006 .
        Familia Pseudodendromonadidae ("Pseudodendromonadaceae") Karpov 2000 , géneros Cyathobodo , Pseudodendromonas .
        Familia Siluaniidae ^(P) (Siluaniaceae) Karpov 1998 , géneros Adriamonas , Siluania , Otto , Regin . ^{[ 97 ]}
        Familia Paramonadidae Kent 1880 , género Paramonas .
        Familia Nanidae Cavalier-Smith en Cavalier-Smith & Scoble 2013 , género Nanum (" Nanos ").
        Familia Neradidae Cavalier-Smith en Cavalier-Smith & Chao 2006 , género Nerada .
        Familia Filidae Cavalier-Smith en Cavalier-Smith & Scoble 2013 , género Filos .
  - Infraphylum incertae sedis
    - Orden Rictida Cavalier-Smith en Cavalier-Smith & Scoble 2013 , familia Rictidae Cavalier-Smith en Cavalier-Smith & Scoble 2013 , género Rictus .
    - Cantina Yubuki y otros, 2015
Subfilo Sagenista Cavalier-Smith 1995
- Clase Labyrinthulea L.S.Olive 1975 ex Cavalier-Smith 1989 (Labyrinthulomycetes Arx 1970 ex Dick 2001 ) (='filo' Labyrinthomorpha Page en Levine et al. 1980 (Labyrinthulomycota Whittaker 1969 ))
  - Orden Amphitremida (Poche 1913) Gomaa et al. 2013
    - Familia Amphitremidae Poche 1913 , géneros Amphitrema , Archerella , Paramphitrema .
    - Familia Diplophryidae Cavalier-Smith en Anderson & Cavalier-Smith 2012 , género Diplophrys .
  - Ordenar Amphifilida Cavalier-Smith en Anderson & Cavalier-Smith 2012 como "Amphifolioidea"
    - Familia Amphifilidae Cavalier-Smith en Anderson & Cavalier-Smith 2012 , género Amphifila .
    - Familia Sorodiplophryidae Cavalier-Smith en Anderson & Cavalier-Smith 2012 , géneros Fibrophrys , Sorodiplophrys .
  - Orden Oblongichytrida (Oblongichytriales) Bennett et al. 2017 , familia Oblongichytriidae (Oblongichytriaceae) Cavalier-Smith en Anderson & Cavalier-Smith 2012 , género Oblongichytrium .
  - Orden Labyrinthulida Doffein 1901 (Labyrinthulales EABessey 1950 )
    - Familia Aplanochytriidae (Aplanochytriaceae) Leander ex Cavalier-Smith en Anderson & Cavalier-Smith 2012 , género Aplanochytrium (= Labyrinthuloides ).
    - Familia Labyrinthulidae Cienkowski 1867 (Labyrinthulaceae Haeckel 1868 ), género Labyrinthula (= Pseudoplasmodium , Labyrinthodictyon , Labyrinthorhiza ).
    - Clado a nivel de familia "Stellarchytriidae" ("Stellarchytriaceae"), género Stellarchytrium .
  - Orden Thraustochytrida (Thraustochytriales) Gorrión 1943
    - Familia Althorniidae (Althornidiaceae) Jones & Alderman 1973 , género Althornia .
    - Familia Thraustochytriidae (Thraustochytriaceae) Sparrow ex Cejp 1959 , géneros Aurantiochytrium , Botryochytrium , Japonochytrium , Monorhizochytrium , Parietichytrium , Phycophthorum , ^{[ 98 ]} Schizochytrium , Sicyoidochytrium , Thraustochytrium , Ulkenia .
- Clase Eogyrea Cavalier-Smith 2013 , orden Eogyrida Cavalier-Smith 2018 ^{[ 77 ]} (=clado MAST-6). Géneros no asignados a ningún taxón inferior: Mastreximonas , Vomastromonas . ^{[ 87 ]}
  - Familia Pseudophyllomitidae (Pseudophyllomitaceae) Shiratori et al. 2017 , género Pseudophyllomitus . ^{[ 99 ]}

Gyrista

Kaonashiidae Weston, Eglit y Simpson 2023. Kaonashia . ^{[ 100 ]}^{[ 101 ]}
Developea Karpov & Aleoshin 2016 ex Cavalier-Smith 2017 . Cubaremonas Tikhonenkov, Cho y Keeling 2022 ^{[ 102 ]} , Develoamica Prokina et al. 2026 ^{[ 103 ]} , Develocanicus Tikhonenkov, Cho, Mylnikov y Keeling 2022 ^{[ 102 ]} , Develocauda Tikhonenkov, Cho y Keeling 2022 ^{[ 102 ]} , Developarva Prokina et al. 2026 ^{[ 103 ]} , Developayella Tong 1995 , Developorapax Karpov & Aleoshin 2016 , Mediocremonas del Campo y Weiler 2020 ^{[ 104 ]} .
Pirsoniales Cavalier-Smith enmienda de 1998. Prokina et al. 2024 . Bordeauxia Prokina et al. 2024 ; Bullionia Prokina et al. 2024 ; Feodosia Prokina et al. 2024 ; Koktebelia Prokina et al. 2024 ; Noirmoutieria Prokina et al. 2024 ; Pirsonia Schnepf, Debres y Elbrachter 1990 . ^{[ 105 ]}
Pseudohongos Cavalier-Smith 1986 (=Heterokontimycotina MW Dick 1976 , Peronosporomycotina MWDick 2001 ) ^{[ 106 ]}^{: 288}
- Hyphochytrea ^ICZNCavalier-Smith 1986 (Hyphochytriomycetes ^ICNSparrow ex MWDick 1983 )
  - Anisolpidiaceae Karling 1943 emend. Dick 2001 . Anisolpidium Karling 1943 ; Canteriomyces Sparrow 1960 .
  - Hyphochytridiomycetaceae Fischer 1892 enmienda. Karling 1939 . Único género: Hyphochytrium Karling 1939 .
  - Rhizidiomycetaceae Karling 1943 . Latrostium Zopf 1894 ; Rhizidiomyces Zopf 1884 ; Gorrión Rhizidiomycopsis 1960 .
- Peronosporomycetes Dick 2001 (=Peronosporomycetes Winter 1897, enmienda. Dick 1976 ). Incertae sedis: Atkinsiella Vishniac 1958 ; Ciliatomyces Foissner y Foissner 1995 (= Ciliomyces Foissner y Foissner 1986 ); ^{[ 107 ]} Crypticola Humber et al. 1989 ; Ectrogella Zopf 1884 ; Eurychasma Magnus 1905 ; Halodafnea MWDick 1998 ; Haliphtoros Vishniac 1958 ; Haptoglosa Drechsler 1940 ; Lagena Vanterp. & Ledingham 1930 ; Lagenisma Drebes 1968 ; Olpidiopsis Cornu 1872 ; Pontisma S.E. Petersen 1905 ; Sofá Pythiella 1935 ; Rozellopsis Karling 1942 ; Sirolpidium HEPetersen 1905 .
  - Linaje saprolegnialeano Lara en Adl et al. 2019 . Achlya Nees 1823 ; Aphanomyces de Bary 1860 ; Aplanopsis Höhnk 1952 ; Apodachlya Pringsh. 1883 ; Aquastella SL Glockling y DP Molloy 2014 ; Geolegnia Coker y JVHarv. 1925 ; Leptomitus (Roth) C.Agardh 1824 ; Newbya MWDick y MASpencer 2002 ; Pythiopsis de Bary 1888 ; Protoachlya Cocker 1923 ; Salisapilia Hulvey, Nigrelli, Telle, Lamour & Thines 2010 ; Saprolegnia Nees 1823 ; Thraustotheca Humphrey 1893 .
  - Linaje peronosporaliano Lara en Adl et al. 2019 . Albugo (Pers.) Roussel ex Gray 1821 ; Bremia Regel 1843 ; Chlamydomyzium MWDick 1997 ; Halophytopthora H.H.Ho y SCJong 1990 ; Hyaloperonospora constante. en Constante. & J.Fatehi 2002 ; Lagenidium Zopf 1859 ; Myzocytiopsis MWDick 1997 ; Peronospora Corda 1837 ; Plasmopara J. Schröt. 1886 ; Pythium Pringsh. 1858 ; Pseudoperonospora Rostovzez 1903 ; Phytophthora de Bary 1975 ; Phytopythium Abad, De Cock, Bala, Robideau, AMLodhi & Lévesque en Bala et al. 2010 ; Pústula Thines 2005 .
Ochrophyta Cavalier-Smith 1986, enmienda. Cavalier-Smith y Chao 1996 (=Heterokontophyta Guiry, RAAndersen y Moestrup 2023 )
- Chrysista Cavalier-Smith 1986 . Incertae sedis: Chrysoderma C. Billard 1984 nom. inválido. ; Crisomeris Carter 1937 ; Crisonefos W.R.Taylor 1952 ; " Giraudyopsis " Dangeard 1965 nom. inválido. ; ^{[ 108 ]} Rhamnochrysis Wilce y Markey 1974 . ^{[ k ]}
  - Eustigmatophyceae Hibberd & Leedale 1971 ^{[ 112 ]}^{[ l ]}
    - Goniochloridales K.P.Fawley, M.Eliáš y MWFawley 2013 . Goniocloris Geitler 1928 ; Pseudostaurastrum Chodat 1921 ; Tetraedriella Pascher 1930 nom. contras. ; Trachydiscus H. Ettl 1964 ; Trebonskia Přibyl & Procházková 2022 ; ^{[ 115 ]} Vacuolivirida Nakayama, Nakamura, Yokoyama, Shiratori, Inouye e Ishida 2015 .
    - Eustigmatales Hibberd 1981
      - Paraeustigmatos M.W.Fawley, Nĕmcová y KPFawley 2019 ^{[ 116 ]}
      - Eustigmataceae Hibberd 1981 . Ellipsoidion Pascher 1938 ; Clorobotrys Bohlin 1901 ; Eustigmatos Hibberd 1981 ; Pseudocharaciopsis KWLee y Bold 1973 ; Vischeria Pascher 1938 .
      - Monodopsidaceae Hibberd 1981 (incluye Loboceae Hedgewald en Hedgewald, Padisak & Friedl 2007 ). Microcloropsis MWFawley, I.Jameson y KPFawley 2015 ; Monodopsis Hibberd 1981 ; Nannochloropsis Hibberd 1981 ; Pseudotetraedriella Hedgewald en Hedgewald, Padisak y Friedl 2007 .
      - Neomonodaceae R.Amaral, KPFawley, Nĕmcová, T.Ševčíková, Lukešová, MWFawley, LMASantos & M.Eliáš 2020 . Botryochloropsis Preisig y Wilhelm 1989 ; Characiopsella R.Amaral, KPFawley, Nĕmcová, T.Ševčíková, Lukešová, MWFawley, LMASantos & M.Eliáš 2020 ; Munda R.Amaral, KPFawley, Nĕmcová, T.Ševčíková, Lukešová, MWFawley, LMASantos & M.Eliáš 2020 ; Neomonodus R.Amaral, KPFawley, Nĕmcová, T.Ševčíková, Lukešová, MWFawley, LMASantos & M.Eliáš 2020 ; Pseudellipsoidion (Neustupa & Nĕmcová) Nĕmcová enmienda. Amaral et al. 2020 .
  - Clado SII
    - Olisthodiscophyceae Barcytė, Eikrem & M. Eliáš 2021 → Olisthodiscus .
    - Pinguiophyceae Kawachi, Inouye, Honda, O'Kelly, Bailey, Bidigare y RAAndersen 2002 . Glossomastix O'Kelly 2002 ; Phaemonas Honda e Inouye 2002 ; Pinguiochrysis Kawachi 2002 ; Pinguiococcus RAAndersen, D.Potter y JCBailey 2002 ; Polipodocrisis Magne 1975 .
    - Clado SSC ^{[ 113 ]}^{[ 114 ]}
      - Chrysophyceae Pascher 1914 . Taxones de Incertae sedis: Chryososaccus , Chrysosphera , Cyclonexis , Lygynion , Phaeoplaca .
        Cromulinales Pascher 1910 . Cromulina , Chrysomonas .
        Hibberdiales Andersen 1989 . Hibberdia .
        Ocromonadales Pascher 1910 . Spumella , Pedospumella , Ochromonas .
        Paraphysomonadida Scoble & Cavalier-Smith 2014 . Paraphysomonas .
        Synurales Andersen 1987 . Chrysodidymus , Mallomonas , Synura , Tesselaria .
      - Picophagea Cavalier-Smith enmienda de 2006. 2017 ^{[ 117 ]} [Synchromophyceae S.Horn y C.Wilhelm 2007 ]. Chlamydomyxa , Chrysopodocystis , Guanochroma , Leukarachnion , Picophagus , Synchroma .
  - clado SI
    - Raphidophyceae Chadefaud 1950 ex Silva 1980 → orden Chattonellales Throndsen en Tomas 1993 enmienda. Yamaguchi, Nakayama, Murakami & Inouye 2010 (=Vacuolariales Shameel, 2001 ). Chattonella , Fibrocapsa , Goniostomum , Haramonas , Heterosigma , Merotricha , Vacuolaria .
    - Clado PX ^{[ 111 ]}
      - Chrysoparadoxophyceae Wetherbee en Wetherbee et al. 2019 → orden Chrysoparadoxales Wetherbee en Wetherbee et al. 2019 → familia Chrysoparadoxaceae Wetherbee en Wetherbee et al. 2019 . ^{[ 118 ]} Chrysoparadoxa Wetherbee en Wetherbee et al. 2019 ; Nematochrysis Pascher 1925 (= Chrysowaernella Gayral & Lepailleur 1971 ). ^{[ 111 ]}
      - Phaeophyceae Hansgirg 1886 [Kjellman 1891; Pfitzer 1894]
        Ascoseirales Petrov 1964 . Ascoseira .
        Desmarestiales Setchell & Gardner 1925 . Arthrocladia , Desmarestia^(P) , Himantothallus , Phaeurus .
        Dictyotales Bory de Saint-Vincent 1828 . Dictyota , Dilophus , Lobophora , Padina , Stypopodium , Taonia , Zonaria .
        Discosporangiales Kawai et al. 2007 . Choristocarpus , Discosporangio .
        Ectocarpales Bessey 1907, emend. Silva & Reviers 2000 . Adenocystis , Acinetospora , Asterocladon , Asteronema , Chordaria , Ectocarpus , Scytosiphon .
        Fucales Bory de Saint-Vincent 1927 . Ascophyllum , Bifurcaria , Cystoseira , Druvillaea , Fucus , Hormosira , Sargazo , Turbinaria .
        Ishigeales Cho et al. 2004 [Ishigeacea Okamura 1935 ]. Ishige .
        Laminariales Migula 1908 . Akkesiophycus , Alaria , Chorda , Costaria , Laminaria , Lessonia , Pseudochoda .
        Nemodermatales Parente et al. 2008 . Nemoderma .
        Onslowiales Draisma & Prud'homme van Reine 2008 . Onslowia .
        Ralfsiales Nakamura ex Lim & Kawai 2007 . Litoderma , Neoralfsia , Pseudolitoderma , Ralfsia .
        Scytothamnales Peters & Clayton 1998 . Scytothamnus , Splachnidium , Stereocladon .
        Sphacelariales Migula 1908 . Chaetopteris , Halopteris , Stypocaulon , Sphacelaria , Verosphacella .
        Sporochnales Sauvageau 1926 . Bellotia , Carpomitra , Nereia , Sporochonus , Tomaculopsis .
        Syringodermatales Henry 1984 . Syringoderma .
        Tilopteridales Bessey 1907 . Cutleria , Halosiphon , Haplospora , Phaeosiphoniella , Phyllaria , Tilopteris .
      - Phaeosacciophyceae R.A.Andersen, L.Graf y HSYoon en Graf et al. 2020 → pedir Phaeosacciales RAAndersen, L.Graf & HSYoon en Graf et al. 2020 ^{[ 111 ]}
        Phaeosaccionaceae J. Feldmann 1949 . Antarctosaccion Delépine 1970 ; Faeosaccion Farlow 1882 .
        Tetrasporopsidaceae R.A.Andersen, L.Graf y HSYoon en Graf et al. 2020 . Tetrasporopsis Lemmermann 1899 ; Psammochrysis R.Wetherbee en Graf et al. 2020 .
      - Phaeothamniophyceae Andersen & Bailey en Bailey et al. 1998
        Phaeothamniales Bourrelly 1954, enmienda. Andersen y Bailey en Bailey et al. 1998 . Feotamnios .
        Pleurocloridales Ettl 1956 . Pleurocloridella .
      - Schizocladiophyceae Henry, Okuda y Kawai 2003 . Schizocladia .
      - Xanthophyceae Allorge 1930, enmienda. Fritsch 1935 [Heterokontae Lutero 1899 ; Heteromonadea Leedale 1983; Xanthophyta Hibberd 1990 ]
        Tribonematales Pascher 1939 . Botrydium , Bumilleriopsis , Characiopsis , Chloromeson , Heterococcus , Monadus , Ophiocytium , Sphaerosorus , Tribonema , Xanthonema .
        Vaucheriales Bohlin 1901 . Vauchería .
- Diatomista Derelle et al. 2016, enmienda. Cavalier-Smith 2017 [clado SIII]. Taxones incertae sedis: clados ambientales MOCH-1, MOCH-2 y MOCH-4 Massana et al. 2014 .
  - Bolidophyceae Guillou et al. 1999 [Parmales Booth & Marchant 1987 ]. Bolidomonas , Triparma , Tetraparma , Pentalamina .
  - Diatomeas Dumortier 1821 [Bacillariophyta Haeckel 1878 ]
    - Leptocilindrofitina D.G. Mann, en Adl et al. 2019
      - Leptocylindrophyceae D.G. Mann, en Adl et al. 2019 . Leptocylindrus , Tenuicylindrus .
      - Corethrophyceae D.G. Mann, en Adl et al. 2019 . Coretrón .
    - Ellerbeckiophytina D.G. Mann, en Adl et al. 2019 . Ellerbeckia .
    - Probosciophytina D.G. Mann, en Adl et al. 2019. Proboscia .
    - Melosirofitina D.G. Mann, en Adl et al. 2019 . Aulacoseira , Melosira , Hyalodiscus , Stephanopyxis , Paralia , Endictya .
    - Coscinodiscophytina Medlin & Kaczmarska 2004, enmienda. Adl et al. 2019 . Actinoptychus , Coscinodiscus , Actinocyclus , Asteromphalus , Aulacodiscus , Stellarima .
    - Rhizosoleniophytina D.G. Mann, en Adl et al. 2019 . Guinardia , Rhizosolenia , Pseudosolenia .
    - Arachnoidiscophytina D.G. Mann, en Adl et al. 2019. Arachnoidiscus .
    - Bacillariophytina Medlin & Kaczmarska 2004, enmienda. Adl et al. 2019
      - Mediophyceae Jouse & Proshkina-Lavrenko en Medlin & Kaczmarska 2004
        Chaetocerotophycidae Round y RM Crawford en Round et al. 1990, enmienda. Adl et al. 2019 . Chaetoceros , Bacteriastrum , Dactyliosolen , Cerataulina , Hemiaulus , Eucampia , Acanthoceras , Urosolenia , Terpsinoë , Hydrosera .
        Lithodesmiophycidae Round y RM Crawford en Round et al. 1990, enmienda. Adl et al. 2019 . Lithodesmium , Lithodesmioides , Helicotheca , Bellerochea , Ditylum .
        Thalassiosirophycidae Round & RM Crawford en Round et al. 1990 . Thalassiosira , Lindavia , Cyclotella , Stephanodiscus , Cyclostephanos , Discostella , Bacteriosira , Skeletonema , Detonula .
        Cymatosirophycidae Round y RM Crawford en Round et al. 1990 . Cymatosira , Minutocellus , Papiliocellulus , Leyanella , Extubocellulus , Plagiogrammopsis , Campylosira , Brockmanniella , Pierrecomperia .
        Odontellophycidae D. G. Mann, en Adl et al. 2019 . Odontella , Triceratium , Cerataulus , Pleurosira , Pseudauliscus , Amphitetras , Trieres , Mastodiscus .
        Chrysanthemodiscophycidae D.G. Mann, en Adl et al. 2019 . Chrysanthemodiscus , Biddulphiopsis , Trigonium , Isthmia , Lampriscus , Stictocyclus , Ardissonea , Climacosphenia , Toxarium .
      - Biddulphiophyceae D. G. Mann, en Adl et al. 2019
        Biddulphiophycidae Round y RM Crawford en Round et al. 1990, enmienda. Adl et al. 2019 . Biddulfia .
        Attheya T. West 1860
      - Bacillariophyceae Haeckel 1878, enmienda. Adl et al. 2019
        Striatellaceae Kützing 1844 . Striatella , Pseudostriatella .
        Urneidophycidae ^(P?)Medlin 2016 . Plagiogramma , Dimeregramma , Rhaphoneis , Delphineis , Psammoneis , Bleakeleya , Asterionellopsis .
        Fragilariophycidae Round in Round, Crawford & Mann 1990, enmienda. Adl et al. 2019 . Fragilaria , Synedra , Tabellaria , Asterionella , Diatoma , Tabularia , Cyclophora , Astrosyne , Licmophora , Rhabdonema , Grammatophora , Staurosira , Thalassionema .
        Bacillariophycidae D.G. Mann en Round, Crawford & Mann 1990, enmienda. Adl et al. 2019 . Eunotia , Achnanthes , Bacillaria , Nitzschia , Pseudonitzschia , Cylindrotheca , Navicula , Seminavis , Haslea , Pleurosigma , Gyrosigma , Achnanthidium , Cocconeis , Frustulia , Diploneis , Sellaphora , Pinnularia , Gomphonema , Cymbella , Didymosphenia , Phaeodactylum , Amphora , Entomoneis , Epithemia , Surirella , etc.
        Naviculales Bessey 1907
        Stauroneidaceae D.G. Mann en Ronda, Crawford y Mann 1990 . Craticula , Dorofeyukea , Fistulifera , Karayevia , Madinithidium , Parlibellus , Prestauroneis , Stauroneis , Schizostauron . ^{[ 119 ]}
  - Dictyochophyceae Silva 1980 [Silicoflagellata Lemmermann, 1901 ]
    - Dictyochales Haeckel 1894 [Dictyochida Borgert, 1891 ; Dictyochaceae Lemmermann, 1901 ]. Dictyocha .
    - Florenciellales Eikrem, Edvardsen y Throndsen 2007 . ^{[ 120 ]} Florenciella , Verrucophora .
    - Pedinellales Zimmermann et al. 1984 [Ciliophryida Febre-Chevalier, 1985 ; Actinomonadaceae Kent, 1880 ]. Actinomonas , Apedinella , Ciliophrys , Mesopedinella , Palatinella , Pedinella , Pseudopedinella , Pteridomonas .
    - Rhizochromulinales O'Kelly y Wujek 1994 [Rhizocromulinaceae O'Kelly y Wujek, 1994 ]. Rizocromulina .
  - Pelagophyceae Andersen & Saunders 1993
    - Pelagomonadales Andersen y Saunders 1993 . Aureococcus , Pelagococcus , Pelagomonas .
    - Sarcinochrysidales Gayral y Billard 1977
      - Sarcinochrysidaceae Gayral y Billard 1977 . Ankylochrisis , Arachnochrysis , Aureoscheda , Aureoumbra , Nematochrysopsis , Pelagospilus , Pulvinaria , Sarcinochrysis , Sargassococcus .
      - Chrysocystaceae M. Melkonian, HSYoon y RAAndersen 2018 . ^{[ 121 ]} Chrysocystis , Chrysoreinhardia , Sungminbooa .
    - Plocamiomonadales Daugbjerg & Lovejoy 2024 . Plocamiomonas . ^{[ 122 ]}

Alveola

Colponemida ^(P)Cavalier-Smith 1993 enmienda. Adl et al. 2019 (=Protalveolata Cavalier-Smith 1991 enmienda. 2017. Géneros no asignados a familias: Neocolponema Gigeroff et al. 2023 ; Loeffela Gigeroff et al. 2023 ^{[ 123 ]}
- Filo ^{[ m ]} Colponemidia Tikhonenkov et al. 2014 → clase Colponemea Cavalier-Smith 1993 → orden Colponemida Cavalier-Smith 1993 → familia Colponemidae Cavalier-Smith & Chao 2004 . Único género: Colponema Stein 1878 .
- Filo ^{[ m ]} Acavomonidia Tikhonenkov et al. 2014 → clase Acavomonea Tikhonenkov et al. 2014 → orden Acavomonida Tikhonenkov et al. 2014 → familia Acavomonidae Tikhonenkov et al. 2014 . Acavomonas Tikhonenkov et al. 2014 .
- Orden Palustrimonadida Cavalier-Smith 2017 → familia Palustrimonadidae Cavalier-Smith 2017 . Único género: Palustrimonas Patterson & Simpson 1996 .

Myzozoa

Filo ^{[ m ]} Chromerida R.B.Moore et al. 2008 → clase Colpodellophyceae Molinari & Guiry 2023 ^{[ 125 ]} ("crompodélidos") ^{[ 126 ]} → orden Colpodellales ^ICN /Colpodellida ^ICZNCavalier-Smith 1993 enmienda. Adl et al. 2005, 2019 . Género Incertae sedis: Piridium Patten 1936 . ^{[ 127 ]}
- Familia Vitrellaceae Oborník & Lukeš 2011 . Género único: Vitrella Oborník & Lukeš 2011 .
- Familia Colpodellaceae Adl et al. 2019 . Géneros: Colpodella Cienkowsky 1865 ; Chilovora Cavalier-Smith 2004 ; Voromonas Cavalier-Smith 2004 .
- Familia Chromeraceae Oborník & Lukeš 2012 . Género único: Chromera R.B.Moore et al. 2008 .
- Familia Alphamonadaceae ^ICN /Alphamonadidae ^ICZNCavalier-Smith en Cavalier-Smith & Chao 2004 . Único género: Alphamonas Aléxéieff 1918 .
Filo ^{[ m ]} Perkinsozoa Norén & Moestrup en Norén et al 1999 → clase Perkinsea Levine 1978 . Géneros Incertae sedis: Phagodinium Kristiansen 1993 ; Rastrimonas Brugerolle 2003 ; ^{[ n ]} Acrocoelus Fernández, Pardos, Benito & Arroyo 1999 .
- Maranthos Alacid & Reñé 2021 ^{[ 132 ]}
- Familia Pararosariidae Jeon & Park 2021. Único género: Pararosarium Jeon & Park 2021. ^{[ 133 ]}
- Familia Parviluciferaceae Reñé & Alacid 2017 . Géneros: Dinovorax Reñé & Alacid 2017 ; Parvilucifera Norén y Moestrup 1999 ; Snorkelia Reñé & Alacid 2017 ; ^{[ 134 ]} Tuberlatum Jeon & Park 2019 . ^{[ 135 ]}
- Familia Perkinsidae Levine 1978 . Único género: Perkinsus Levine 1978 .
- Familia Xcellidae Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017 em. Karlsbakk, Nystøyl, Plarre y Nylund 2021 . Géneros: Cryoxcellia Evans, Patel, Matzke & Millar 2023 , ^{[ 136 ]} Gadixcellia Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017 ; Notoxcellia Desvignes et al. 2022 ; ^{[ 137 ]} Salmoxcellia Karlsbakk, Nystøyl, Plarre & Nylund 2021 ; ^{[ 138 ]} Xcellia Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017 .
Filo ^{[ m ]} Dinoflagellata Bütschli 1885, enmienda. Fensome et al. 1993, enmienda. Adl et al. 2005 . Géneros de Incertae sedis: de vida libre ( Adenoides , Akashiwo , Amphidiniella , Ankistrodinium , Apicoporus , Archaeosphaerodiniopsis , Bispinodinium , Bysmatrum , Cabra , Cladopyxis , Crypthecodinium , Cucumeridinium , Dactylodinium , Dicroerisma , Gloeodinium , Grammatodinio , Gynogonadinio , Gyrodiniellum , Halostylodinium , Heterodinium , Moestrupia , Paragymnodinium , Phytodinium , Plagiodinium , Planodinium , Pileidinium , Pseudadenoides , Pseudothecadinium , Pyramidodinium , Rhinodinium , Roscoffia , Sabulodinium , Sphaerodinium , Spiniferodinio , Testudodinio , Tecadinio , Thecadiniopsis , Togula ) y el parásito Blastodiniales Chatton 1906 [ya no es válido] ( Amyloodinium , Apodinium , Cachonella , Caryotoma , Crepidoodinium , Haplozoon , Oodinium , Myxodinium , Piscinoodinium , Protoodinium , Rhinodinium , Schyzochitriodinium , Stylodinium ).
- Psammosa Okamoto, A. Horák y Keeling 2012 ^{[ 139 ]}^{[ 140 ]}
- Familia Oxyrrhinaceae Sournia 1984 . Género único: Oxyrrhis Dujardin 1841 . ^{[ 140 ]}
- Eleftheros Tikhonenkov, Hehenberger y Keeling 2023 ^{[ 140 ]}
- Clase Endodinea Cavalier-Smith 2017 → orden Ichthyodinida Cavalier-Smith 2017 (grupo alveolar marino ambiental I) ^{[ 140 ]}
  - Familia Hobagellidae Yoo, Kim y Wayne Coats 2024. Único género: Hobagella Yoo, Kim y Wayne Coats 2024. ^{[ 141 ]}
  - Familia Euduboscquellidae Coats & Bachvaroff 2012 . Euduboscquella DWCoats, TRBachvaroff y CFDelwiche 2012 ; Dogelodinium Loeblich y ARLoeblich 1966 nom. contras. ; Keppenodinium Loeblich y ARLoeblich 1966 nom. contras. (= Hollandella Cachón 1964 ).
  - Familia Ichthyodiniidae Cavalier-Smith 2017 . Único género: Ichthyodinium Hollande & Cachon 1952 .
- Clase Ellobiopsea A.R.Loeblich 1976 → orden Ellobiopsida Whisler 1990 → familia Ellobiopsidae Coutière 1911 . Géneros: Ellobiopsis Caullery 1910 ; Thalassomyces Niezabitowski 1913 ; Parallobiopsis B.Collin 1913 ; Ellobiocystis Coutière 1911 ; Rhizellobiopsis Hovasse 1926 . ^{[ o ]}
- Clase Syndiniophyceae ^ICN /Syndinea ^ICZNA.R.Loeblich 1976 → orden Syndiniales A.R.Loeblich 1976
  - Familia Amoebophryaceae ^ICN /Amoebophryidae ^ICZNCachon 1964 (Grupo II de alveolados marinos ambientales). Único género: Amoebophrya Koeppen 1892 .
  - Familia Syndiniaceae ^ICN /Syndinidae ^ICZNChatton 1910 (Grupo IV de alveolados marinos ambientales). Hematodinium , Syndinium , Solenodinium .
  - Familia Sphaeriparaceae AR Loeblich 1970 . Géneros: Atlanticellodinium J.Cachon y M.Cachon-Enjumet 1965 ; Sphaeripara Poche 1911 nominado. contras.
- Clase Noctiluciphyceae Fensome et al. 1993 → orden Noctilucales Haeckel 1894 . Abedinium , Cachonodinium , Craspedotella , Cymbodinium , Kofoidinium , Leptodiscus , Noctiluca , Petalodinium , Pomatodinium , Scaphodinium , Spatulodinium .
- Clase Dinophyceae Pascher 1914
  - Subclase Gymnodiniphycidae Fensome et al. 1993
    - Gymnodiniales F. Stein 1878, enmienda. G. Hansen y Moestrup en Daugbjerg et al. 2000 en sentido estricto . Barrufeta , Chytriodinium , Dissodinium , Erythropsidinium , Greuetodinium , Gymnodinium , Lepidodinium , Nematodinium , Nusuttodinium , Pellucidodinium , Polykrikos , Proterythropsis , Wangodinium , ^{[ 143 ]} Warnowia .
    - Amphidinium Claparède & Lachmann 1859, enmienda. Flø Jørgensen et al. 2004 en sentido estricto
    - Gyrodinium Kofoid & Swezy 1921, enmienda. G. Hansen y Moestrup en Daugbjerg et al. 2000 en sentido estricto
    - Kareniaceae Bergholtz et al. 2005 . Braquidinio , Karenia , Karlodinio , Takayama .
    - Ceratoperidiniaceae Loeblich III 1980, enmienda. Reñé & de Salas 2013 . Ceratoperidinio , Kirithra .
    - Torodiniales Boutrup, Moestrup & Daugbjerg 2016 . Kapelodinio , Torodinio .
    - Levanderina Moestrup et al. 2014
    - Margalefidinio F. Gómez, Richlen & DM Anderson 2017
    - Cochlodinium F. Schütt enmienda. F. Gómez, Richlen & DM Anderson 2017 sensu estricto
    - Ptychodiscales Fensome et al. 1993 . Achradina , Amphilothus , Balechina , Ptychodiscus , Sclerodinium .
    - Borghiellaceae Moestrup, Lindberg y Daugbjerg 2009 . Baldinia , Borghiella .
    - Tovelliaceae Moestrup et al. 2005 . Bernardinio , Esoptrodinio , Jadwigia , Tovellia .
    - Suessiaceae Fensome et al. 1993, enmienda. Moestrup et al. 2009 . Ansanella , Asulcocephalium , Biecheleria , Biecheleriopsis , Leiocephalium , Pelagodinium , Polarella , Prosoaulax , Protodinium , Symbiodinium , Yihiella .
  - Subclase Peridiniphycidae Fensome et al. 1993
    - Gonyaulacales Taylor 1980 . Alexandrium , Amylax , Ceratium , Ceratocorys , Coolia , Fukuyoa , Fragilidium , Gambierdiscus , Goniodoma , Gonyaulax , Lingulodinium , Ostreopsis , Pentaplacodinium , Peridiniella , Protoceratium , Pyrocystis , Pyrodinium , Pyrophacus , Tripos .
    - Peridiniales Haeckel 1894 . Amphidiniopsis , Archaeperidinium , Blastodinium , Diplopelta , Diplopsalis , Diplopsalopsis , Herdmania , Niea , Oblea , Palatinus , Parvodinium , Peridinium , Peridiniopsis , Preperidinium , Protoperidinium , Qia , Vulcanodinium .
    - Thoracosphaeraceae Schiller 1930 . Aduncodinium , Amyloodinium , Apocalathium , Blastodinium , Chimonodinium , Cryptoperidiniopsis , Duboscquodinium , Ensiculifera , Laciniporus , ^{[ 144 ]} Leonella , Luciella , Naiadinium , Paulsenella , Pentapharsodinium , Pfiesteria , Scrippsiella , Stoeckeria , Theleodinium , Thoracosphaera , Tintinnophagus , Tyrannodinium .
    - Podolampadaceae Lindemann 1928 . Blepharocysta , Gaarderiella , Heterobractum , Lissodinium , Mysticella , Podolampas .
    - Kryptoperidiniaceae Lindemann 1925 ["dinotomas"]. Blixaea , Durinskia , Galeidinium , Kryptoperidinium , Unruhdinium , etc.
    - Heterocapsaceae Fensome et al. 1993 . Heterocapsa .
    - Amphidomataceae Sournia 1984 . Anfidoma , Azadinio .
    - Oxytoxaceae Lindemann 1928 . Corythodinium , Oxytoxum .
    - Centrodiniaceae Hernández-Becerril 2010 . Centrodinio .
  - Dinofisales Kofoid 1926 . Anfisolenia , Citaristes , Dinofurcula , Dinophysis , Histioneis , Latifascia , Metadinophysis , Metaphalacroma , Ornithocercus , Oxyphysis , Parahistioneis , Phalacroma , Pseudophalacroma , Sinophysis , Triposolenia .
  - Prorocentrales Lemmermann 1910 . Mesoporus , Prorocentrum .
Clase Squirmidea Cavalier-Smith 2014. Digyalum , Filipodium , Platyproteum . ^{[ 145 ]}^{[ 146 ]}
Filo ^{[ m ]} Apicomplexa Levine 1980, enmienda. Adl et al. 2005 . Géneros Incertae sedis: Aggregata ^{[ p ]} Frenzel 1885 , Christalloidophora Dehorne 1934 , Dobellia Ikeda 1914 , Echinococcidium Porchet 1978 , Globidiellum Brumpt 1913 , Joyeuxella Brasil 1902 , Rhabdospora Laguesse 1906 , Spermatobium Eisen 1895 , Spiriopsis Arvy y Peters 1972 , Spirogregarina Wood y Herman 1943 , Toxocystis Léger y Duboscq 1910 , Trophosphaera Le Calvez 1939 .
- Orden Agamococcidiorida Levine 1979 (=Histogregarida Cavalier-Smith 2014 )
  - Familia Gemmocystidae Upton & Peters 1986 . Único género: Gemmocystis .
  - Familia Rhytidocystidae Levine 1979 . Único género: Rhytidocystis .
- Orden Protococcidiorida Kheisin 1956 (=Coelotrophiida Vivier 1982 ). Angeiocystis , Coelotropha , Grellia , Eleutheroschizon , Mackinnonia , Myriosporides , Myriospora , Sawayella .
- Aconoidasida ^(P)Mehlhorn, Peters & Haberkorn 1980 (=Hematozoa Vivier 1982 )
  - Orden Haemospororida Danielewsky 1885 . Dionisia , Haemocystidium , Haemoproteus , Hepatocystis , Leucocytozoon , Mesnilium , Nycteria , Parahaemoproteus , Plasmodium , Polychromophilus , Rayella , Saurocytozoon .
  - Orden Piroplasmida Wenyon 1926 . Anthemosoma , Babesia , Cytauxzoon , Echinozoon , Haemohormidium , Sauroplasma , Serpentoplasma , ^{[ 148 ]}^{[ 149 ]} Theileria .
  - Orden Nephromycida Cavalier-Smith 1993, emend. Adl et al. 2019 . Nephromyces , Cardiosporidium .
- Conoidasida ^(P)Levine 1988
  - Orden Corallicolida Kwong et al. 2021 → familia Corallicolidae Kwong et al. 2021 . Géneros: Corallicola Kwong et al. 2021 ; Anthozoaphila Kwong et al. 2021 ; Gemmocystis Upton y Peters 1986 . ^{[ 150 ]}
  - Coccidia Leuckart 1879 ^(P)
    - Suborden Adeleorina Léger 1911 . Adelea , Adelina , Babesiosima , Bartazoon , Chagasella , Cyrilia , Dactylosoma , Desseria , Ganapatiella , Gibbsia , Haemogregarina , Haemolivia , Hepatozoon , Ithania , Karyolysus , Klossia , Klossiella , Legerella , Orcheobius , Rasajeyna .
    - Suborden Eimeriorina Léger 1911 . Atoxoplasma , Barrouxia , Besnoitia , Caryospora , Caryotropha , Choleoeimeria , Cyclospora , Cystoisospora , Defretinella , Diaspora , Dorisa , Dorisiella , Eimeria , Elleipsisoma , Goussia , Hammondia , Hyaloklossia , Isospora , Lankesterella , Mantonella , Merocystis , Neospora , Nephroisospora , Ovivora , Pfeifferinella , Pseudoklossia , Sarcocystis , Schellackia , Selenococcidium , Selysina , Spirocystis , Toxoplasma , Tyzzeria , Wenyonella .
  - Gregarínida Dufour 1828 . Taxones Incertae sedis: Digyalum Koura et al. 1990 , Exoschizon Hukui 1939 .
    - Archigregarinorida Grassé 1953 ^(P) . Meroselenidium , Merogregarina , Selenidium , Selenocystis , Veloxidium .
    - Eugregarinorida Léger 1900 ^(P) . Apolocystis , Amoebogregarina , Ancora , Ascogregarina , Asterophora , Blabericola , Caliculium , Cephaloidophora , Colepismatophila , Cystobia , Cystocephalus , Difficilina , Diplauxis , Enterocystis , Ganímedes , Geneiorhynchus , Gonospora , Gregarina , Heliospora , Hentschelia , Hirmocystis , Hoplorhynchus , Lankesteria , Lecudina , Leidyana , Lithocystis , Monocystella , Monocystis , Nematopsis , Nematocystis , Neoasterophora , Paralecudina , Paraschneideria , Phyllochaetopterus , Pileocephalus , Polyplicarium , Polyrhabdina , Porospora , Prismatospora , Protomagalhaensia , Psychodiella , Pterospora , Pyxinia , Pyxinioides , Rhabdocystis , Sphaerorhynchus , Steinina , Stenophora , Stylocephalus , Sycia , Syncystis , Thalicola , Thiriotia , Trichotokara , Uradiophora , Urospora , Xiphocephalus , Zygosoma y más.
    - Neogregarinorida Grassé 1953 . Apicystis , Aranciocystis , Caulleryella , Coelogregarina , Farinocystis , Gigaductus , Lipocystis , Lipotropha , Lymphotropha , Machadoella , Mattesia , Menzbieria , Ophryocystis , Schizocystis , Syncystis , Tipulocystis .
    - Cryptogregarinorida Cavalier-Smith 2014, enmienda. Adl et al. 2019 . Criptosporidio .
  - Clase Blastogregarinea Chatton y Villeneuve 1936, emend. Simdyanov et al. 2018 . Chattonaria , Siedleckia .

Ciliophora

Postciliodesmatophora Gerassimova y Seravin 1976
- Karyorelictea Corliss 1974
  - Kentrophoridae Jankowski 1980 . Kentrophoros .
  - Loxodida Jankowski 1980
    - Cryptopharyngidae Jankowski 1980 . Criptofaringe .
    - Loxodidae Bütschli 1889 . Loxodes .
  - Geleiidae Kahl 1933 . Geleia .
- Heterotrichea Stein 1859
  - Blepharismidae Jankowski en Small & Lynn 1985. Blepharisma
  - Climacostomidae Repak 1972 . Climacostomum .
  - Condylostomatidae Kahl en Doflein y Reichenow 1929 . Chattonidium , Condilostoma .
  - Fabreidae Shazib et al. 2014 . Fabrea .
  - Gruberiidae Shazib et al. 2014 . Gruberia .
  - Coliphorina Jankowski 1967
    - Folliculinidae Dons 1914 . Folliculina .
    - Maristentoridae Miao et al. 2005 . Maristentor .
  - Peritromidae Stein 1867 . Peritromo .
  - Spirostomidae Stein 1867 . Anigsteinia , Spirostomum .
  - Stentoridae Carus 1863 . Estentor .
Intramacronucleata Lynn 1996 . Taxones Incertae sedis: Protocruziidae Jankowski 1980 [Protocruziidia de Puytorac et al. 1987 ] ( Protocruzia Faria da Cunha & Pinto 1922 ).
- SAL Gentekaki et al. 2014 . Taxones Incertae sedis: Cariacotrichea Orsi et al. 2011 ( Cariacothrix caudata ), Mesodiniidae ankowski, 1980 ( Mesodinium ), Phacodiniidia Small y Lynn 1985 ( Phacodinium ).
  - Espirotriquea Bütschli 1889
    - Euplotia Jankowski 1979
      - Euplotida Small y Lynn 1985
        Aspidiscidae Ehrenberg 1830 . Aspidisca .
        Certesiidae Borror & Hill 1995 . Certesia .
        Euplotidae Ehrenberg 1838 . Euplotes .
        Gastrocirrhidae Fauré-Fremiet 1961 . Gastrocirro .
        Uronychidae Jankowski 1975 . Diofris , Uronichia .
      - Discocephalida
        Discocephalidae Jankowski 1979 . Discocephalus , Prodiscocephalus , Paradiscocephalus .
        Pseudoamphisiellidae Song et al. 1997 . Leptoamphisiella , Pseudoamphisiella .
    - Perilemmaphora Berger 2008
      - Hipotriquia Stein 1859
        Stichotrichida Fauré-Fremiet 1961 ^(P)^{[ q ]}
        Amphisielidae Jankowski 1979 . Amphisiella , Bistichella .
        Atractosidae Bourland 2015 . Atractos .
        Epiclintidae Wicklow & Borror 1990 . Epiclintes .
        Gonostomatidae Small & Lynn 1985 . Cotterillia , Gonostomum .
        Halteriidae Claparède y Lachmann 1858 . Halteria , Meseres .
        Holostichidae Fauré-Fremiet 1961 . Holosticha , Uncinata .
        Kahliellidae Tuffrau 1979 . Deviata , Kahliella .
        Keronidae Dujardin 1840 . Kerona .
        Oxytrichidae Ehrenberg 1830 ^(P) . Cyrtohymena , Gastrostyla , Oxytricha , Stylonychia .
        Parabirojimidae Dai y Xu 2011 . Parabirojimia , Tunicothrix .
        Plagiotomidae Bütschli 1887 . Plagiotoma .
        Psammomitridae Jankowski 1979 . Psammomitra .
        Pseudoamphisiellidae Song et al. 1996 . Pseudoamphisiellidae .
        Psilotrichidae Bütschli 1889 . Psilotricha , Urospinula .
        Schmidingerotrichidae Foissner 2012 . Schmidingerothrix .
        Spirofilidae von Gelei 1929 . Spirofilopsis , Strongylidium .
        Trachelostylidae Small & Lynn 1985 . Trachelostyla .
        Uroleptidae Foissner & Stoeck 2008 . Paruroleptus , Uroleptus .
        Urostylida Jankowski 1979 ^(P)
        Bergeriellidae Liu et al. 2010 . Bergeriella , Neourostylopsis .
        Hemicycliostylidae Lyu et al. 2018 . Australothrix , Hemicycliostyla .
        Pseudokeronopsidae Borror & Wicklow, 1983 . Apoholosticha , Pseudokeronopsis .
        Pseudourostylidae Jankowski 1979 . Pseudourostyla .
        Urostylidae Bütschli 1889 . Bakuella , Diaxonella , Urostyla .
      - Oligotrichea Bütschli 1887
        Oligotricida Bütschli 1887
        Cyrtostrombidiidae Agatha 2004 . Cyrtostrombidium .
        Pelagostrombidiidae Agatha 2004 . Pelagostrombidio .
        Strombidiidae Fauré-Fremiet 1970 . Estrombidio^(P) .
        Tontonidae Agatha 2004 . Labea , Tontonia .
        Choreotrichida Small y Lynn 1985 . Taxones Incertae sedis: Lynnella Liu et al. 2011 [Lynnellidae Liu et al. 2011 ; Lynnellida Liu et al. 2015 ]
        Strobilidiina Jankowski 1980 ^(P)
        Leegaardiellidae Lynn y Montagnes 1988 . Leegaardiella .
        Lohmanniellidae Montagnes & Lynn 1991 . Lohmanniella .
        Strobilidiidae Kahl en Doflein y Reichenow 1929 . Estrobilidio .
        Strombidinopsidae Small & Lynn 1985 . Strombidinopsis^(P) .
        Tintínina Kofoid y Campbell 1929 . Taxones de Incertae sedis: Helicostomella , Tintinnopsis^(P) , varios otros géneros.
        Ascampbelliellidae Corliss 1960 . Ascampbelliella
        Cyttarocylididae Kofoid & Campbell 1929 [probablemente sinónimo de Petalotrichidae]. Cyttarocylis .
        Dictyocystidae Haeckel 1873 . Dictyocysta .
        Epiplocylididae Kofoid & Campbell 1939 . Epiplocylis .
        Eutintinnidae Bachy et al. 2012 . Dartintinnus , Eutintinnus .
        Favellidae Kofoid & Campbell 1929 . Favella .
        Nolaclusiliidae Sniezek et al. 1991 . Nolaclusilis .
        Petalotrichidae Kofoid & Campbell 1929 [probablemente sinónimo de Cyttarocylididae]. Petalotricha .
        Ptychocylididae Kofoid & Campbell 1929 . Cymatocylis , Ptychocylis .
        Rhabdonellidae Kofoid & Campbell 1929 . Metacylis , Rhabdonella , Schmidingerella .
        Stenosemellidae Campbell 1954 ^(P) . Stenosemella .
        Tintinnidae Claparède & Lachmann 1858 . Amphorellopsis , Salpingacantha , Salpingella , Tintinnus .
        Tintinnidiidae Kofoid & Campbell 1929 . Tintinnidium .
        Undellidae Kofoid y Campbell 1929 . Undela .
        Xystonellidae Kofoid & Campbell 1929 . Dadayiella , Parafavella , Xystonella .
    - Licnophoridae Bütschli 1887 . Licnophora , Prolicnophora .
    - Kiitrichidae Nozawa 1941 . Caryotricha , Kiitricha .
  - Lamellicorticata Vd'ačný et al. 2010
    - Armophorea Lynn 2004 . Taxones Incertae sedis: Mylestomatidae Kahl en Doflein & Reichenow, 1929 ( Mylestoma ).
      - Metopida Jankowski 1980 ^(P)
        Metopidae Kahl 1927 ^(P) . Bothrostoma , Brachonella , Eometopus , Metopus , Parametopidium , Tesnospira .
        Apometopidae Foissner 2016 . Cirranter , Urostomides .
        Tropidoatractidae Rotterová et al. 2018 . Palmarella , Tropidoatractus .
      - Clevelandellida de Puytorac & Grain 1976
        Clevelandellidae Kidder 1938 . Clevelandella .
        Inferostomatidae Ky 1971 . Inferostoma .
        Neonyctotheridae Affa'a 1987 . Neonyctotherus .
        Nyctotheridae Amaro 1972 ^(P) . Nyctoterio .
        Sicuophoridae Amaro 1972 . Sicuófora .
      - Caenomorphidae Poche 1913 . Caenomorpha , Ludio , Sulfonecta .
      - Odontostomatida Sawaya 1940
        Discomorphellidae Corliss 1960 . Discomorphella .
        Epalxellidae Corliss 1960 . Epalxella , Saprodinium .
    - Litostomatea Pequeño & Lynn 1981
      - Rhynchostomatia Jankowski 1980
        Dileptida Jankowski 1978
        Diléptidos Jankowski 1980 . Apodileptus , Dileptus , Pseudomonilicaryon .
        Dimacrocaryonidae Jankowski 1978 . Dimacrocaryon , Monomacrocaryon , Rimaleptus .
        Tracheliidae Ehrenberg 1838 . Trachelius .
      - Haptoria Corliss 1974 ^(P) . Taxones Incertae sedis: Chaenea .
        Lacrymariidae de Fromentel 1876 . Lacrymaria .
        Haptorida Corliss 1974
        Enchelyodonidae Foissner et al. 2002 . Enchelyodon , Fuscheria .
        Homalozoonidae Jankowski 1980 . Homalozoon .
        Pleuroplitidae Foissner 1996 . Pleuroplites .
        Didiniidae Poche 1913 . Didinio , Monodinio .
        Pleurostomatida Schewiakoff 1896
        Amphileptidae Bütschli 1889 . Amphileptus .
        Litonotidae Kent 1882 . Litonoto .
        Kenphilidae Wu et al. 2015 . Epiphyllum , Kentophyllum .
        Spathidiida Foissner y Foissner 1988
        Acropisthiidae Foissner y Foissner 1988 . Acropistio , Chaenea .
        Actinobolinidae Kahl 1930 . Actinobolina .
        Apertospathulidae Foissner et al. 2005 . Apertospatula .
        EnchelyidaeEhrenberg 1838 . Enchelys .
        Pseudoholophryidae Berger et al. 1984 . Pseudoholophrya .
        Spathidiidae Kahl en Doflein y Reichenow 1929 . Legendrea , ^{[ 151 ]} Spathidium .
        Trachelophyllidae Kent 1882 . Trachelophyllum .
        Helicoprorodontidae Small & Lynn 1985
      - Trichostomatia Bütschli 1889
        Vestibuliferida de Puytorac et al. 1974
        Balantidiidae Reichenow en Doflein y Reichenow 1929 . Balantidio , Neobalantidio^(P) .
        Buetschliidae Poche 1913 . Buetschlia .
        Paraisotrichidae da Cunha 1917 . Paraisotricia .
        Protocaviellidae Grain en Corliss 1979 . Protocaviella .
        Protohalliidae da Cunha y Muniz 1927 . Protohallia .
        Pycnotrichidae Poche 1913 . Pycnothrix , quizás Buxtonella .
      - Isoendo
        Isotrichidae Bütschli 1889 . Dasytricha , Isotricha .
        Entodiniomorphida Reichenow en Doflein & Reichenow 1929
        Blepharocorythina Wolska 1971
        Blepharocorythidae Hsiung 1929 . Blepharocorys .
        Parentodiniidae Ito, Miyazaki e Imai 2002 . Parentodinio .
        Pseudoentodiniidae Wolska 1986 . Pseudoentodinio .
        Entodiniomorphina Reichenow en Doflein & Reichenow 1929
        Cycloposthiidae Poche 1913 . Cycloposthiium .
        Gilchristinidae Ito, Ishihara & Imai 2014 [Gilchristidae Ito et al. 2006 ]. Digilchristia , Gilchristina . ^{[ 152 ]}
        Ophryoscolecidae Stein 1859 . Entodinium , Ophryoscolex , Polyplastron .
        Polydiniellidae Corliss 1960 . Polydiniella .
        Rhinozetidae Van Hoven, Gilchrist y Hamilton-Attwell 1988 . Rhinozeta .
        Spirodiniidae Strelkow 1939 . Spirodinium .
        Telamodiniidae Latteur y Dufey 1967 . Telamodinio .
        Troglodytellidae Corliss 1979 . Troglodytella ,.
        Macropodiniida Lynn 2008
        Amylovoracidae Cameron & O'Donoghue 2002 . Amylovorax .
        Macropodiniidae Dehority 1996 . Macropodinium .
        Polycostidae Cameron & O'Donoghue 2003 . Polycosta .
- CONTHREEP Lynn en Adl et al. 2012 [Ventrata Cavalier-Smith 2004 ]. Taxones de Incertae sedis: Askenasia Blochmann 1895 , Cyclotrichiidae Jankowski 1980 ( Cyclotrichium ), Paraspathidium Noland 1937 , Pseudotrachelocercidae Song 1990 ( Pseudotrachelocerca ), Discotrichidae Jankowski 1967 [Discotrichida Fan et al. 2014 ] ( Discotricha , Lópezoterenia ).
  - Filofaríngea de Puytorac et al. 1974
    - Synhymeniida de Puytorac et al. en Deroux 1978
      - Nassulopsidae Deroux en Corliss 1979 . Nassulopsis .
      - Orthodonellidae Jankowski 1968 . Orthodonella , Zosterodasys .
      - Scaphidiodontidae Deroux en Corliss 1979 . Chilodontopsis , Scaphidiodon .
      - Synhymeniidae Jankowski en Small & Lynn 1985 . Synhymenia .
    - Subkinetalia Gong et al. 2009
      - Cyrtophoria Fauré-Fremiet en Corliss 1956
        Chlamydodontida Deroux 1976 ^(P)
        Chilodonellidae Deroux 1970 . Chilodonella .
        Chitonellidae Small & Lynn 1985 . Chitonella .
        Chlamydodontidae Stein 1859 . Chlamydodon .
        Gastronautidae Deroux 1994 . Gastronauta .
        Kryoprorodontidae Alekperov & Mamajeva 1992 . Gymnozoum .
        Lynchellidae Jankowski 1968 . Chlamydonella , Lynchella .
        Disteria Deroux 1976
        Dysteriidae Claparède y Lachmann 1858 . Disteria^(P) , Trochilia .
        Hartmannulidae Poche 1913 ^(P) . Hartmannula .
        Kyaroikeidae Sniezek & Coats 1996 . Kyaroikeus .
        Plesiotrichopidae Deroux 1976 . Plesiotricopus .
        Chonotrichia Wallengren 1895
        Exogemmida Jankowski 1972
        Chilodochonidae Wallengren 1895 . Chilodochona .
        Filichonidae Jankowski 1973 . Filichona .
        Helichonidae Jankowski 1972 . Heliochona .
        Lobochonidae Jankowski 1967 . Lobochona .
        Phyllochonidae Jankowski 1972 . Phyllochona .
        Spirochonidae Stein 1854 . Spirochona .
        Criptogemmida Jankowski 1975
        Actinichonidae Jankowski 1973 . Actinichona .
        Equinichonidae Jankowski 1973 . Equinicona .
        Inversochonidae Jankowski 1973 . Inversochona .
        Isochonidae Jankowski 1973 . Isochona .
        Isochonopsidae Batisse & Crumeyrolle 1988 . Isochonopsis .
        Stylochonidae Mohr 1948 . Stylochona .
      - Rincodia Chatton & Lwoff 1939
        Hypocomidae Bütschli 1889 . Hipocoma .
        Rhynchodida Chatton & Lwoff 1939
        Ancistrocomidae Chatton & Lwoff 1939 . Ancistrocoma .
        Sphenophryidae Chatton & Lwoff 1921 . Sphenophrya .
      - Suctoria Claparède & Lachmann 1858
        Exogenida Collin 1912
        Allantosomatidae Jankowski 1967 . Allantosoma .
        Dentacinetidae Batisse 1992 . Dentacineta .
        Dendrosomididae Jankowski 1978 . Dendrosomides .
        Ephelotidae Kent 1882 . Ephelota .
        Lecanophryidae Jankowski 1973 . Lecanophrya .
        Manuelophryidae Dovgal 2002 . Manuelophrya .
        Metacinetidae Bütschli 1889 . Metacineta .
        Ophryodendridae Stein 1867 . Ophryodendron .
        Paracinetidae Jankowski 1978 . Paracineta .
        Phalacrocleptidae Kozloff 1966 . Phalacrocleptes .
        Podophryidae Haeckel 1866 . Podophrya .
        Praethecacinetidae Dovgal 1996 . Praethecacineta .
        Rhabdophryidae Jankowski 1970 . Rabdofria .
        Severonidae Jankowski 1981 . Severonis .
        Spelaeophryidae Jankowski en Batisse 1975 . Spelaeophrya .
        Tachyblastonidae Grell 1950 . Tachyblaston .
        Thecacinetidae Matthes 1956 . Thecacineta .
        Endogenida Collin 1912
        Acinetidae Stein 1859 . Acineta .
        Acinetopsidae Jankowski 1978 . Acinetopsis .
        Choanophryidae Dovgal 2002 . Choanofria .
        Corynophryidae Jankowski 1981 . Corynophrya .
        Dactylostomatidae Jankowski 1978 . Dactylostoma .
        Dendrosomatidae Fraipont 1878 . Dendrosoma .
        Endosphaeridae Jankowski en Corliss 1979 . Endosphaera .
        Erastophryidae Jankowski 1978 . Erastophrya .
        Pseudogemmidae Jankowski 1978 . Pseudogemma .
        Rhynchetidae Jankowski 1978 . Rhyncheta .
        Solenophryidae Jankowski 1981 . Solenophrya .
        Tokophryidae Jankowski en Small & Lynn 1985 . Tokophrya .
        Trichophryidae Fraipont 1878 . Trichophrya .
        Evaginogenida Jankowski en Corliss 1979
        Cometodendriidae Jankowski 1978 . Cometodendron .
        Cyathodiniidae da Cuhna 1914 . Ciatodinio .
        Dendrocometidae Haeckel 1866 . Dendrocometes .
        Discophryidae Collin 1912 . Discofria .
        Enchelyomorphidae Augustin y Foissner 1992 . Enchelyomorfa .
        Heliophryidae Corliss 1979 . Heliophrya .
        Periacinetidae Jankowski 1978 . Periacineta .
        Prodiscophryidae Jankowski 1978 . Prodiscophrya .
        Rhynchophryidae Jankowski 1978 . Rhynchophrya .
        Stylocometidae Jankowski 1978 . Stylocometes .
        Trypanococcidae Dovgal 2002 . Trypanococcus .
  - Colpodea Small y Lynn 1981
    - Bursariomorphida Fernández-Galiano 1978
      - Bryometopidae Jankowski 1980 . Bryometopus(P) , Thylakidium .
      - Bursaridiidae Foissner 1993 . Bursaridium , Paracondylostoma .
      - Bursariidae Bory de San Vicente 1826 . Bursaria .
    - Colpodida de Puytorac et al. 1974 . Taxones Incertae sedis: Bardeliellidae Foissner 1984 ( Bardeliella ), Hausmanniellidae Foissner 1987 ( Avestina , Hausmanniella ), Ilsiellidae Bourland et al. 2011 ( Ilsiella ), Pseudochlamydonellidae Buitkamp et al. 1989 ( Hackenbergia , Pseudochlamydonella ) y Marynidae Poche 1913 ( Marina ).
      - Bryophryina de Puytorac et al. 1979
        Bryophryidae de Puytorac et al. 1979 . Briofria .
        Sandmanniellidae Foissner & Stoeck 2009 . Sandmanniella .
      - Colpodina Foissner et al. 2011
        Colpodidae Bory de St. Vincent 1826 ^(P) . Colpoda .
        Granoriidae Corliss 1960 . Grandoria .
        Tillinidae Foissner et al. 2011 . Tillina .
      - Grossglockneriidae Foissner 1980 [Grossglockneriina Foissner 1980 ]. Grossglockneria , Pseudoplatyophrya .
    - Cyrtolophosida Foissner 1978
      - Cyrtolophosididae Stokes 1888 . Cyrtolophosis .
      - Kreyellidae Foissner 1979 . Kreyella .
    - Platyophryida de Puytorac et al. 1979
      - Ottowphryidae Foissner et al. 2011 . Ottowphrya , Platyophryides .
      - Platyophryidae de Puytorac et al. 1979 ^(P) . Platiofria .
      - Sagittariidae Grandori y Grandori 1935 . Sagitario .
      - Sorogenidae Bradbury & Olive 1980 . Sorogena .
      - Woodruffiidae Gelei 1954 . Etoschophrya , Rostrophrya , Woodruffia .
  - Nassophorea ^(P)
    - Colpodidiidae Foissner 1995 . Colpodidium .
    - Nassulida Jankowski 1967
      - Furgasoniidae Corliss 1979 . Furgasonia , Wolfkosia .
      - Nassulidae de Fromentel 1874 . Nassula , Obertrumia .
    - Microthoracida Jankowski 1967
      - Microthoracidae Wrzesniowski 1870 . Drepanomonas , Microtórax .
      - Leptopharyngidae Kahl 1926 . Leptopharynx , Pseudomicrothorax .
  - Prostomatea Schewiakoff 1896 ^(P)
    - Apsiktratidae Foissner et al. 1994 [Prostomatida Schewiakoff 1896 ]
      - Balanionidae pequeño y Lynn 1985 . Balanión .
      - Cryptocaryonidae Wright & Colorni 2002 . Cryptocaryon .
      - Colepidae Ehrenberg 1838 . Coleps , Plagiopogon .
      - Holophryidae Perty 1852 . Holophrya .
      - Lagynidae Sola et al. 1990 . Lagynus .
      - Metacystidae Kahl 1926 . Metacystis , Vasicola .
      - Placidae pequeño y Lynn 1985 . Placo .
      - Plagiocampidae Kahl 1926 . Plagiocampa .
      - Prorodontidae Kent 1881 . Prorodon .
      - Urotrichidae Small & Lynn 1985 . Urotricha .
  - Plagiopylea Small y Lynn 1985
    - Plagiopylida Small y Lynn 1985
      - Epalxellidae Corliss 1960 . Epalxella , Saprodinium .
      - Plagiopylidae Schewiakoff 1896 . Plagiopyla .
      - Sonderiidae pequeños y Lynn 1985 . Sondería .
      - Trimyemidae Kahl 1933 . Trimyema .
  - Oligohymenophorea de Puytorac et al. 1974
    - Apostomatia Chatton & Lwoff 1928
      - Apostomatida Chatton & Lwoff 1928
        Colliniidae Cépède 1910 . Collinia , Metacollinia .
        Cyrtocaryidae Corliss 1979 . Cyrtocaryum .
        Foettingeriidae Chatton 1911 . Foettingeria .
        Pseudocolliniidae Chantangsi et al. 2013 . Fusiforma , Pseudocollinia .
      - Astomatóforida Jankowski 1966
        Opalinopsidae Hartog 1906 . Opalinopsis .
      - Pilisuctorida Jankowski 1966
        Conidophryidae Kirby 1941 . Conidophrys .
    - Astomatia Schewiakoff 1896
      - Anoplophryidae Cépède 1910 . Anoplofria .
      - Buetschliellidae de Puytorac en Corliss 1979 . Bütschliella .
      - Clausilocolidae de Puytorac en Corliss 1979 . Clausilocola .
      - Contophryidae de Puytorac 1972 . Contofira .
      - Haptophryidae Cépède 1923 . Haptophrya .
      - Hoplitophryidae Cheissin 1930 . Hoplitophrya .
      - Intoshellinidae Cépède 1910 . Intoshellina .
      - Maupasellidae Cépède 1910 . Maupasella .
      - Radiophryidae de Puytorac 1972 . Radiophrya .
    - Hymenostomatia Delage y Hérouard 1896
      - Tetrahymenida Fauré-Fremiet en Corliss 1956 . Taxones Incertae sedis: Trichospiridae Kahl 1926 ( Trichospira ).
        Curimostomatidae Jankowski 1968 . Curimostoma .
        Glaucomidae Corliss 1971 . Glaucoma .
        Spirozonidae Kahl 1926 . Espirozona .
        Tetrahymenidae Corliss 1952 . Tetrahymena .
        Turaniellidae Didier 1971 . Colpidium , Dexiostoma , Turaniella .
      - Ophryoglenida Canella 1964
        Ichthyophthiriidae Kent 1881 . Ichthyophthirius .
        Ophryoglenidae Kent 1881 . Ophryoglena .
    - Peniculia Fauré-Fremiet en Corliss 1956 ^(P)
      - Peniculida Fauré-Fremiet en Corliss 1956
        Clathrostomatidae Kahl 1926 . Clathrostoma .
        Frontonidae Kahl 1926 . Disematostoma , Frontonia^(P) .
        Lembadionidae Jankowski en Corliss 1979. Lembadion .
        Maritujidae Jankowski en Small y Lynn 1985 . Marituja .
        Neobursaridiidae Dragesco & Tuffrau 1967 . Neobursaridium .
        Parameciidae Dujardin 1840 . Paramecio .
        Paranassulidae Fauré-Fremiet 1962 . Paranasula .
        Stokesiidae Roque 1961 . Stokesia .
        Urocentridae Claparède & Lachmann 1858 [Urocentridae de Puytorac, Grain & Mignot 1987 ]
    - Peritrichia Stein 1859
      - Sessilida Kahl 1933
        Astylozoidae Kahl 1935 . Astilozoon , Hastatella .
        Ellobiophryidae Chatton y Lwoff 1929 . Ellobiophrya .
        Epistylididae Kahl 1933 . Epístilis .
        Lagenophryidae Bütschli 1889 . Lagenophrys .
        Operculariidae Fauré-Fremiet en Corliss 1979 . Opercularia .
        Rovinjellidae Matthes 1972 . Rovinjella .
        Scyphidiidae Kahl 1933 ^(P) . Escifidia .
        Termitopryidae Lom en Corliss 1979 . Termitoprya .
        Usconophryidae Clamp 1991 . Usconophrys .
        Vaginicolidae de Fromentel 1874 . Cothurnia , Pyxicola , Thuricola , Vaginicola .
        Vorticellidae Ehrenberg 1838 . Carchesium , Epicarchesium^(P) , Ophrydium , Pelagovorticella , Pseudovorticella^(P) , Vorticella^(P) .
        Zoothamniidae Sommer 1951 . Haplocaulus , Zoothamnium .
      - Mobilida Kahl 1933
        Polycyclidae Poljansky 1951 . Polycycla .
        Trichodinidae Claus 1874 . Trichodina .
        Trichodinopsidae Kent 1881 . Trichodinopsis .
        Urceolariidae Dujardin 1840 . Leiotrocha , Urceolaria .
    - Escuticociliatia Pequeña 1967 ^(P)
      - Filasterida Pequeña 1967
        Cohnilembidae Kahl 1933 . Cohnilembus .
        Cryptochilidae Berger en Corliss 1979. Cryptochilum .
        Entodiscidae Jankowski 1973 . Entodiscus .
        Entorhipidiidae Madsen 1931 . Entorhipidio .
        Orchitophryidae Cépède 1910 ^(P) . Orchitophrya .
        Paralembidae Corliss & de Puytorac en Small & Lynn 1985 . Anophrys , Paralembus .
        Parauronematidae Small y Lynn 1985 ^(P) . Parauronema^(P) .
        Filasteridae Kahl 1931 . Kahlilembus , Filáster .
        Pseudocohnilembidae Evans & Thompson 1964 . Pseudocohnilembus .
        Schizocaryidae Jankowski 1979 . Schizocaryum .
        Thigmophryidae Chatton & Lwoff 1926 . Thigmophrya .
        Thyrophylacidae Berger en Corliss 1961 . Thyrophylax .
        Uronematidae Thompson 1964 . Uronema .
        Urozonidae Grolière 1975 . Urozona .
      - Pleuronemátida Fauré-Fremiet en Corliss 1956
        Calyptotrichidae Small & Lynn 1985 . Calyptotricha .
        Conchophthiridae Kahl en Doflein y Reichenow 1929 . Conchophthirus .
        Ctedoctematidae Small & Lynn 1985 . Ctedoctema .
        Cyclidiidae Ehrenberg 1838 ^(P) . Cristigera , Cyclidium .
        Dragescoidae Jankowski 1980 . Dragescoa .
        Eurystomatellidae Miao et al. 2010 . Eurystomatella .
        Histiobalantiidae de Puytorac & Corliss en Corliss 1979 . Histiobalantium .
        Peniculistomatidae Fenchel 1965 . Peniculistoma .
        Pleuronematidae Kent 1881 ^(P) . Pleuronema .
        Thigmocomidae Kazubski 1958 . Thigmocoma .
      - Thigmotrichida Chatton & Lwoff 1922
        Ancistridae Issel 1903 . Ancistro .
        Hemispeiridae König 1894 . Hemispeira .
        Hysterocinetidae Diesing 1866 . Hysterocineta .
        Paraptychostomidae Ngassam et al. 1994 . Paraptychostomum .
      - Loxocephalida Jankowski 1964 ^(P)
        Cinetochilidae Perty 1852 ^(P) . Cinetochilum , Sathrophilus .
        Loxocephalidae Jankowski 1964 . Cardiostomatella , Dexiotricha , Loxocephalus .

Rhizaria

Incertae sedis taxa: Gymnosphaerida Poche 1913, enmienda. Mikrjukov 2000 . Actinocoryne , Cienkowskya , Gymnosphaera , Hedraiophrys [posible sinónimo de Cienkowskya ], Wagnerella .

Cercozoa

Incertae sedis taxa:
- Géneros de ubicación incierta: Discocelia , Kraken , Dictiomyxa , Katabia , Myxodictyium , Pontomyxa , Protomyxa , Protogenes , Pseudospora , Rhizoplasma .
- Psammonobiotidae Golemansky 1974, enmienda. Meisterfeld 2002 . Alepiella , Chardezia , Edaphonobiotus , Feuerbornia , Frenzelina , Lesquerella , Micramphora , Micropsammella , Nadinella , Ogdeniella , Psammonobiotus , Propsammonobiotus , Rhumbleriella .
- Volutellidae Sudzuki, 1979 . Pseudovolutella , Volutella .
Aquavolonida Bass & Berney 2018 . Aquavolon , Lapot . ^{[ 153 ]}
Tremulida Howe et al. 2011 . Trémula .
Cercomonadida Poche 1913, enmienda. Vickerman 1983, enmienda. Mylnikov 1986, enmienda. Karpov et al. 2006; modificar Howe et al. 2009; enmienda Cavalier-Smith 2012 , Cercomonas , Eoercomonas , Filomonas , Neocercomonas , Cavernomonas .
Paracercomonadida Cavalier-Smith 2018 [Paracercomonadidae Cavalier-Smith & Karpov 2012 ]. Brevimastigomonas , Metabolomonas , Nucleocercomonas , Paracercomonas , Phytocercomonas .
Glissomonadida ^(P)^{[ 154 ]} Howe & Cavalier-Smith 2009 [Heteromitidae Kent 1880, emend. Mylnikov 1990, emend. Mylnikov & Karpov 2004 ]. Género no asignado a ningún taxón inferior: Neuromorpha . ^{[ 154 ]}
- Saccharomycomorphidae Feng, He, Jiang, Zhang y Yu 2021 . Saccharomycomorpha^(P) . ^{[ 155 ]}
- Viridiraptoridae Hess & Melkonian 2013 . Orciraptor , Viridiraptor .
- Sandonidae ^(P)^{[ 156 ]} Howe et al. 2009 . Sandona^(P)^{[ 156 ]} , Flectomonas , Neoheteromita^(P)^{[ 155 ]} , Mollimonas .
- Dujardinidae Howe & Cavalier-Smith 2011 . Dujardina^(P)^{[ 154 ]} .
- Bodomorphidae ^(P)^{[ 156 ]} Hollande 1952, enmienda. Cavalier-Smith en Howe et al. 2009 . Bodomorfa^(P)^{[ 156 ]} .
- Proleptomonadidae Howe et al. 2009 . Proleptomonas .
- Allapsidae ^(P)^{[ 154 ]} Howe & Cavalier-Smith 2009 . Allapsa^(P)^{[ 155 ]} , Teretomonas , Allantion .
Pansomonadida ^{[ 157 ]} Vickerman en Vickerman et al. 2005 . Agitata , Aurigamonas .
Sainouroidea Cavalier-Smith en Cavalier-Smith et al. 2009 [Helkesida Cavalier-Smith 2018 ]
- Sainouridae ^(P)Cavalier-Smith 2008 . Acantholus , Cholamonas , Homocognata , Sainouron .
- Helkesimastigidae Cavalier-Smith 2008 . Helkesimastix .
- Guttulinopsidae Oliva 1970 . Guttulinopsis , Olivorum , Puppisaman , Rosculus .
Thecofilosea Cavalier-Smith 2003, enmienda. Cavalier-Smith 2011 . Taxones incertae sedis: Mataza .
- Phaeodarea Haeckel 1879 [Tripylea Hertwig 1879 ]
  - Feoconchia Haeckel 1879 . Coelodendrum , Coelographis , Conchellium , Conchopsis .
  - Phaeocystina Haeckel 1879 . Aulacantha , Aulographis , Cannoraphis .
  - Phaeogromia Haeckel 1879 . Castanella , Challengeron , Haeckeliana , Medusetta , Tuscarora .
  - Phaeosphaeria Haeckel 1879 . Aulosphaera , Cannosphaera , Sagosphaera .
- Cryomonadida Cavalier-Smith 1993
  - Rhogostomidae Dumack et al. 2017 . Rhogostoma , Sacciforma , Capsellina .
  - Protaspidae Cavalier-Smith 1993 [Cryomonadidae Cavalier-Smith 1993 ]. Cryothecomonas , Protaspa .
- Ventricleftida Cavalier-Smith 2011
  - Ventrifissuridae Cavalier-Smith 2018 . Ventrifissura .
  - Verrucomonadidae Cavalier-Smith 2018 . Verrucomonas .
- Tectofilósida Cavalier-Smith 2003
  - Chlamydophryidae De Saedeleer, 1934 . Chlamydophrys Cienkowski 1876 , Diaphoropodon Archer 1869 , Lecythium Hertwig & Lesser 1874 , Katarium Solbach 2024 , ^{[ 158 ]} Trachyrhizium Shiratori & Ishida 2016 .
  - Fiscullidae Dumack, Mausbach y Bonkowski en Dumack et al. 2017 . Fisculla , Omnívora . ^{[ 159 ]}
  - Pseudodiflugiidae De Saedeleer 1934 . Pseudodiflugia , Lenkorania . ^{[ 160 ]}
  - Rhizaspididae Skuja 1948 . Rhizaspis .
- Ebriacea Lemmermann 1901 [Ebriidae Poche 1913 ; Ebríida Deflandre 1936 ]. Ebria , Hermesinum , Botuliforma .
Imbricatea Cavalier-Smith 2011
- Spongomonadida Hibberd 1983 [Spongomonadidae Karpov 1990 ]. Rhipidodendron , Spongomonas .
- Marimonadida Cavalier-Smith & Bass 2011
  - Abolliferidae Cavalier-Smith 2018. Abollifer , Cowlomonas y probablemente Heterochromonas .
  - Auranticordidae Cavalier-Smith 2018 . Auranticordis , Rhabdamoeba .
  - Cyranomonadidae Cavalier-Smith 2018 . Cyranomonas .
  - Pseudopirsoniidae Cavalier-Smith 2018 . Pseudopirsonia .
- Variglissida Cavalier-Smith 2014
  - Clautriaviidae Cavalier-Smith en Cavalier-Smith y Scoble, 2013 . Clautriavia .
  - Nudifilidae Cavalier-Smith en Howe et al., 2011 . Nudifila .
  - Quadriciliidae Cavalier-Smith 2018 . Quadricilia .
- Thaumatomonadida Shirkina 1987 [Thaumatomastigidae Patterson y Zoelfell 1991 ]
  - Thaumatomonadidae Hollande 1952 . Allas , Hyaloselene , Reckertia , Thaumatomonas , Thaumatomastix , Ovaloplaca , Scutellomonas , Thaumatospina , Penardeugenia .
  - Peregriniidae Cavalier-Smith 2011 . Gyromitus , Peregrinia .
  - Esquamulidae Shiratori, Yabuki e Ishida 2012 . Esquamula .
- Euglyphia Cavalier-Smith 2018 Incertae sedis taxa: Zoelucasa .
  - Euglyphida Copeland 1956, enmienda. Cavalier-Smith 1997 . Taxones de Incertae sedis: Phaeobola . ^{[ 161 ]}
    - Cyphoderiidae de Saedeleer 1934 . Campascus , Corythionella , Cyphoderia [ Schaudinnula ], Messemvriella , Pseudocorythion , Ichthyosquama , Knarr , Oleiformis , Psammoderia . ^{[ 162 ]}
    - Paulinellidae de Saedeleer 1934, enmienda. Adl et al. 2012 . Micropyxidiella , Ovulinata , Paulinella .
    - Euglyphina Kosakyan y otros, 2016
      - Assulinidae Lara et al. 2007 . Assulina , Placocista , Valkanovia .
      - Sphenoderiidae Chatelain et al. 2013 . Sphenoderia , Trachelocorythion , Deharvengia .
      - Trinematidae Hoogenraad & De Groot 1940, enmienda Adl et al. 2012 . Corythion , Playfairina , Puytoracia , Trinema .
      - Euglyphidae Wallich 1864, enmienda Lara et al. 2007 . Euglifa , Scutiglifa .
      - Tracheleuglifo ^{[ r ]} Deflandre 1928
  - Trivalvulariida Siemensma & Dumack 2020 . ^{[ 163 ]} Leptogromía trivalvular .
Metromonadea Cavalier-Smith 2007, emend. Cavalier-Smith 2011 . Metromonas , Metopion , Micrometopion , Kiitoksia .
Granofilosea Cavalier-Smith & Bass 2009 . ^{[ 164 ]} Incertae sedis taxa: Apogromia , Kibisidytes , Leucodictyon , Limnofila , Mesofila , Microcometes , Microgromia , Nanofila , Reticulamoeba y probablemente Belaria , Ditrema , Heliomorpha [= Dimorpha ] y Paralieberkuehnia .
- Massisteridae Cavalier-Smith 1993 . Massisteria , Minimassisteria .
- Clathrulinidae Claus 1874 [Desmothoracida Hertwig y Lesser 1874 ]. Actinosphaeridium , Cienkowskya , Clathrulina , Hedriocystis , Penardiophrys , Servetia .
Chlorarachnea Hibberd & Norris 1984 . Amorphochlora , Bigelowiella , Chlorarachnion , Cryptochlora , Gymnochlora , Lotharella , Minorisa , Partenskyella , Viridiuvalis .

Endomyxa Cavalier-Smith enmienda de 2002. Bass y Berney en Adl et al. 2019
- Vampyrellida West 1901, enmienda. Hess y cols. 2012 [Aconchulinida De Saedeleer 1934 ]. Taxones de Incertae sedis: Arachnula , Gobiella , Lateromyxa , Penardia . ^{[ 165 ]}
  - Thalassomyxa Grell 1985
  - Vampyrellidae Zopf 1885 . Vampyrell .
  - Leptophryidae Hess, Sausen y Melkonian 2012 . Arachnomyxa , Leptophrys , Planctomyxa , Platyreta , Pseudovampyrella , ^{[ 166 ]} Theratromyxa , Vernalophrys .
  - Placopodidae Jahn 1928 [Hyalodiscidae Poche 1913 ]. Placopus .
  - Sericomyxidae Más, Simpson & Hess 2021 . Sericomixa .
- Phytomyxea Engler y Prantl 1897
  - Marinomyxa Kolátková, Čepička, Hoffman y Vohník 2021 ^{[ 167 ]}
  - Plasmodiophorida Cook 1928 [Plasmodiophorales Engl. 1892 ; ^{[ 168 ]} Plasmodiophoromycota RH Whittaker 1969 ^{[ 1 ]} ]. Plasmodiophora [ Ostenfeldiella ], Polymyxa , Woronina , Ligniera [ Anisomyxa ; Rhizomyxa ; Sorolpidium ], Sorosphaerula [ Tuburcinia ; Sorosporium ], Spongospora [ Clathrosorus ], Membranosorus , Octomyxa , Polymyxa , Sorodiscus , Tetramyxa [ Molliardia ; Thecaphora ]. ^{[ 169 ]}^{[ 170 ]}^{[ 171 ]}
  - Phagomyxida Cavalier-Smith 1993 . Phagomyxa , Maullinia .
- Filoreta Bass y Cavalier-Smith 2009
- Gromia Dujardin 1835
- Viscidocauda Shiratori y Ken-ichiro 2025 ^{[ 172 ]}
- Ascetosporea Sprague 1979, enmienda. Cavalier-Smith 2009
  - Haplosporida Caullery & Mesnil 1899 . Bonamia , Haplosporidium , Minchinia , Urosporidium .
  - Mikrocytida Hartikainen et al. 2013 . Mikrocitos , Paramikrocitos .
  - Paramyxida Chatton 1911 . Marteilia , Paramyxa , Paramarteilia , Marteiloides , Eomarteilia .
  - Claustrosporidium Larsson 1987
  - Paradiniida Schiller 1935 . Paradinium .

Foraminíferos

Los foraminíferos , o foraminíferos, son un grupo diverso de amebas acuáticas unicelulares, que generalmente poseen una pared orgánica o calcárea, y que suman más de 6700 especies vivas y muchos taxones fósiles. ^{[ 174 ]} Originalmente fueron clasificados como un orden de protozoos (Foraminiferida) perteneciente a la ahora obsoleta Granoreticulosa, junto con otras amebas reticulosas. Posteriormente, la mayoría de los protozoólogos los separaron en su propio filo, aunque los micropaleontólogos los mantuvieron como una clase, ^{[ 175 ]} hasta que fueron ubicados como un subfilo del filo Retaria junto con los Radiolarios. ^{[ 77 ]} Se dividen en tres clases (o subclases, cuando se tratan globalmente como una clase): los monotalámicos parafiléticos , ^{[ 176 ]} que contienen amebas con paredes orgánicas de una sola cámara y algunas amebas desnudas (por ejemplo, los grandes xenofióforos ); y los grupos monofiléticos Globothalamea y Tubothalamea , que evolucionaron a partir de monotalámicos, cada uno con amebas con conchas multicamerales, orgánicas o calcáreas. ^{[ 173 ]} Se han propuesto algunos sistemas alternativos para dividir los foraminíferos en clases, ^{[ 177 ]} pero ninguno ha logrado consenso. Las relaciones de los monotalámicos siguen siendo objeto de estudio debido a la limitada cantidad de datos genéticos. ^{[ 173 ]}

La clasificación de los foraminíferos se compiló numerosas veces a lo largo del siglo XX, culminando en 1987 con el catálogo de géneros de foraminíferos publicado por los paleontólogos Alfred R. Loeblich Jr. y Helen Tappan . ^{[ 178 ]} Posteriormente, se han publicado catálogos individualmente para grupos separados de foraminíferos en función de su morfología y ecología. Dos clasificaciones para géneros de foraminíferos exclusivamente aglutinados (de pared orgánica) se publicaron en 2001 ^{[ 175 ]} y 2014, ^{[ 179 ]} y una clasificación para foraminíferos planctónicos se publicó en 2022. ^{[ 180 ]}

Subfilo Foraminifera d'Orbigny 1826

¿ Lagenida ^?
¿ Heterogromia^?
^¿Komokiaceae *
Clase Monothalamea ^(P)Haeckel 1862 sensu Pawlowski et al. 2013 ('monotalamidas'). ^{[ 176 ]} Géneros no asignados a ningún taxón inferior: Adhaerentella , ^{[ 181 ]} Astrammina , Bathysiphon , Bowseria , ^{[ 182 ]} Crithionina , Flaviatella , ^{[ 183 ]} Notodendrodes , Psammophaga , Leannia , ^{[ 184 ]} Nujappikia . ^{[ 185 ]}
- Familia Lieberkuehniidae Siemensma et al. 2021 , géneros Lieberkuehnia , Claparedellus . ^{[ 186 ]}
- Familia Edaphoallogromiidae Siemensma et al. 2021 , género Edaphoallogromia . ^{[ 186 ]}
- Familia Lacogromiidae Siemensma & Holzmann 2021 , género Lacogromia . ^{[ 186 ]}
- Familia Limnogromiidae Holzmann & Siemensma 2021 , género Limnogromia . ^{[ 186 ]}
- Familia Schizamminidae Nørvang, 1961 , géneros Jullienella , Schizammina , Spiculosiphon . ^{[ 187 ]}
- Familia Velamentofexidae Völcker & Clauß 2021 , género Velamentofex . ^{[ 186 ]}
- Orden Allogromiida ^(P)Hartog en Harmer & Shipley 1906
  - Familia Allogromiidae Rhumbler 1904 , géneros Allogromia , Vellaria . ^{[ 188 ]}
  - Familia Reticulomyxidae Página 1987 enmienda. Hülsmann 2014 , géneros Reticulomyxa , Dracomyxa , Haplomyxa , Wobo . ^{[ 189 ]}
  - Familia Lagynidae Schultze 1854 , géneros Apogromia , Belaria , Boderia , Cystophrys , Heterogromia
- Orden Astrorhizida Lankester 1885
  - Suborden Astrorhizina Lankester 1885
    - Superfamilia Xenophyophoroidea Tendal 1972 , géneros Abyssalia , Aschemonella , Bizarria , Claraclippia , Galatheammina , Homogammina , Moanammina , Psammina , Reticulammina , Rhizammina , Semipsammina , Shinkaiya , Spiculammina , Stannophyllum , Stereodiktyoma , Syringammina , Tendalia . ^{[ 190 ]}^{[ 191 ]}^{[ 192 ]}^{[ 193 ]}^{[ 194 ]}

Clase Tubothalamea Pawlowski et al. 2012 . † Fusulinida Delage & Hérouard 1896 probablemente pertenece a este grupo. ^{[ 10 ]}
- Orden Miliolida Delage & Hérouard 1896 . Alveolina , Cornusspira , Miliammina , Pyrgo , Quinqueloculina , Sorites .
- Orden Spirillinida Hohenegger y Piller 1975 . Patelina , Spirillina .
- Familia Ammodiscidae Reuss 1862. Ammodiscus , Glomospira .

Clase Globothalamea Pawlowski et al. 2012
- Orden Loftusiida Kaminski 2004
  - Suborden Biokovinina Kaminski 2004
    - Superfamilia Biokovinoidea Gušić 1977
      - Family CharentiidaeLoeblich & Tappan 1985, genera Charentia, Ismailia, Karaisella, Melathrokerion, Moncharmontia, Praekaraisella, Praepeneroplis.
    - Superfamily CoscinophragmatoideaThalmann 1951
      - Family HaddoniidaeSaidova 1981, genera Haddonia, Stylonina.
      - Family CoscinophragmatidaeThalmann 1951, genera Alpinophragmium, Ammotrochoides, Bdelloidina, Goellipora, Coscinophragma.
  - Suborder LoftusiinaKaminski & Mikhalevich 2004
    - †Superfamily HaplophragmioideaEimer & Fickert 1899
      - †Family CribratinidaeLoeblich & Tappan 1964, genera Cribratina, Sievoides.
      - †Family HaplophragmiidaeEimer & Fickert 1899, genus Haplophragmium.
      - †Family LabyrinthidomatidaeLoeblich & Tappan 1987, genera Bulbophragmium, Labyrinthidoma.
    - Superfamily LoftusioideaBrady 1884
      - Family CyclamminidaeMarie 1941
        Subfamily AlveolophragmiinaeSaidova 1981, genera Alveolophragmium, †Popovia, †Quasicyclammina, †Reticulophragmoides, Reticulophragmium, †Sabellovoluta.
        †Subfamily BuccicrenatinaeLoeblich & Tappan 1985, genus Buccicrenata.
        †Subfamily ChoffatellinaeMaync 1958, genera Abuhammadina, Bramkampella, Choffatella, Paracyclammina, Torinosuella.
        Subfamily CyclammininaeMarie 1941, genus Cyclammina.
        †Subfamily HemicyclammininaeBanner 1966, genera Alveocyclammina, Flabellamminopsis, Hemicyclammina.
        †Subfamily PseudochoffatellinaeLoeblich & Tappan 1985, genera Balkhania, Broeckinella, Dhrumella, Montsechiana, Pseudochoffatella, Torremiroella.
      - †Family EcougellidaeLoeblich & Tappan 1985, genus Ecougella.
      - †Family EverticyclamminidaeSeptfontaine 1988, genera Everticyclammina, Rectocyclammina.
      - †Family HottingeritidaeLoeblich & Tappan 1985, genus Hottingerita.
      - †Family LoftusiidaeBrady 1884, genera Loftusia, Praereticulinella, Reticulinella.
      - †Family MesoendothyridaeVoloshinova 1958
        †Subfamily MesoendothyrinaeBanner 1966, genera Audienusina, Mesoendothyra.
        †Subfamily LabyrinthininaeSeptfontaine 1988, genus Labyrinthina.
        †Subfamily LevantinellinaeFourcade, Mouty & Teherani 1997, genus Levantinella.
        †Subfamily PlaniseptinaeSeptfontaine 1988 nom. nud., genera Planisepta, Paleomayncina, Orbitammina, Orbitopsella.
      - †Family RamalhoidaeSchlagintweit 2024, genus Ramalhoa.^[195]
      - †Family SpirocyclinidaeMunier-Chalmas 1887, genus Martiguesia, Pseudospirocyclina, Qataria, Reissella, Saudia, Sornayina, Spirocyclina, Sreptocyclammina, Thomasella, Vania.
      - †Family SuraqalatiidaeSchlagintweit & Rashidi 2018, genus Suraqalatia.^[196]
      - †Family SyrianidaeKaminski 2004, genus Syriana.
  - Suborder OrbitolininaKaminski 2004
    - †Superfamily PfenderinoideaSmout & Sugden 1962
      - †Family BakhtiarellidaeSchlagintweit & Rashidi 2022, genus Bakhtiarellia.^[197]
      - †Family HauraniidaeSeptfontaine 1988
        †Subfamily AmijellinaeSeptfontaine 1988, genera Alveosepta, Alzonella, Alzonorbitopsella, Amijiella, Anchispirocyclina, Bostia, Ijdranella, Kastamonina, Palaeocyclammina, Pseudocyclammina, Redmondellina, Spiraloconulus.
        †Subfamily HauraniinaeSeptfontaine 1988, genera Cymbriaella, Gutnicella, Haurania, Meyendorffina, Platyhaurania, Socotraina, Timidonella.
- Order RotaliidaDelage & Hérouard 1896
  - Family PlanorbulinidaeSchwager 1877. Planorbulinella, Hyalinea.
  - Superfamily DiscorboideaEhrenberg 1838
    - Family DiscorbidaeEhrenberg 1838. Discorbis.
    - Family RosalinidaeReiss 1963. Rupertina, Discanomalina, "Rosalina", Gavelinopsis, Planorbulina.
  - Superfamily RotalioideaEhrenberg 1839, emend. Pawlowski 2013. Genera incertae sedis: Criboelphidium, "Elphidium", Protelphidium.
    - Family ElphidiidaeGalloway 1933, genus Elphidium.
    - Family AmmoniidaeSaidova 1981, genus Ammonia.
    - Family ElphidiellidaeHolzmann & Pawlowski 2017, genus Elphidiella.
    - Family HaynesinidaeMikhalevich 2013, genera Haynesina, Aubignyna.
  - Superfamily GlabratelloideaLoeblich & Tappan 1964
    - Family RotaliellidaeLoeblich & Tappan 1964, genera Rotaliella, Rossyatella.
    - Family BuliminoididaeSeiglie 1970, genus Buliminoides.
    - Family GlabratellidaeLoeblich & Tappan 1964, genera Glabratella, Glabratellina, Angulodiscorbis, Planoglabratella.
  - Superfamily CalcarinoideaSchwager 1876
    - Family CalcarinidaeSchwager 1876, genera Neorotalia, Baculogypsina, Baculogypsinoides, Schlumbergerella, Pararotalia.
  - Superfamily Nummulitoideade Blainville 1827, family Nummulitidaede Blainville 1827, genera Nummulites, Operculinella, Cycloclypeus, Heterostegina, Operculina, Planoperculina, Planostegina.
  - Superfamily SerioideaHolzmann & Pawlowski 2017
    - Family UvigerinidaeHaeckel 1894, genera Uvigerina, Rectuvigerina, Trifarina.
    - Family BolivinitidaeGlaessner 1937, genera Bolivina, Brizalina, Saidovina.
    - Family Cassidulinidaed'Orbigny 1839, genera Globocassidulina, Cassidulinoides, Evolvocassidulina, Islandiella, Ehrenbergina
    - Family SphaeroidinidaeCushman 1927, genus Sphaeroidina.
    - Family GlobobuliminidaeCushman 1927, genus Globobulimina.
  - Incertae sedis families
    - ^?Family NonionidaeSchultze 1854, genera Nonion, Nonionella, Nonionellina, Nonionoides.
    - ^?Family VirgulinellidaeLoeblich & Tappan 1984, genus Virgulinella.
    - ^?Family BuliminidaeJones 1875, genus Bulimina.
    - ^?Family EpistominellidaeHolzmann & Pawlowski 2017, genus Epistominella.
    - ^?Family StainforthiidaeReiss 1963, genera Stainforthia, Gallitellia.
    - ^?Family CibicididaeCushman 1927, genera Cibicides, Cibicidoides, Heterolepa.
    - ^?Family ChilostomellidaeBrady 1881, genus Chilostomella.
    - ^?Family PullenidaeSchwager 1877, genus Pullenia.
    - ^?Family NuttalidaeSaidova 1981, genus Nuttalides.
    - ^?Family DiscorbinellidaeSigal 1952, genera Discorbinella, Hanzawaia.
    - ^?Family AstrononionidaeCushman & Edwards 1937, genus Astrononion.
    - ^?Family OridorsalidaeLoeblich & Tappan 1984, genus Oridorsalis.
    - ^?Family MelonidaeHolzmann & Pawlowski 2017, genus Melonis.
    - ^?Family CymbaloporidaeCushman 1927, genus Cymbaloporella.
    - ^?Family RubratelliidaeHolzmann & Pawlowski 2017, genus Rubratella.
    - ^?Family MurrayinelliidaeHolzmann & Pawlowski 2017, genus Murrayinella.
- Order Globigerinida^(P)Lankester 1885 emend. Arz, Arenillas & Gilabert 2022^[180]
  - †Superfamily ParvularugoglobigerinoideaArenillas, Arz & Gilabert 2022
    - †Family ParvularuglobigerinidaeArenillas, Arz & Gilabert 2022, genera Pseudocaucasina, Palaeoglobigerina, Parvularugoglobigerina.
  - Superfamily EoglobigerinoideaBouDagher-Fadel 2012
    - †Family EoglobigerinidaeBlow 1979, genera Alicantina, Eoclavatorella, Eoglobigerina, Parasubbotina, Pseudoglobigerinella, Subbotina, Turbeogloborotalia.
    - Family GloboquadrinidaeBlow 1979, genera Dentoglobigerina, Globoquadrina.
    - †Family NeoacarininidaeBouDagher-Fadel 2012, genus Neoacarinina.
    - †Family PorticulasphaeridaeBanner 1982, genera Globigerinatheka, Guembelitrioides, Inordinatosphaera, Orbulinoides, Porticulasphaera.
  - Superfamily GlobigerinoideaCarpenter, Parker & Jones 1862
    - Family GlobigerinidaeCarpenter, Parker & Jones 1862, genera Alloglobigerinoides, Ciperoella, Globigerina, Globicuniculus, Globigerinoides, Globigerinoidesella, Globoturborotalita, Trilobigerina (=Trilobatus), Zeaglobigerina.
    - Family GlobigerinellidaeBouDagher-Fadel 2012, genera Beella, Bolliella, Globigerinella, Orcadia, Protentella, Quiltyella.
    - Family HastigerinidaeBolli, Loeblich & Tappan 1957, genera Hastigerina, Hastigerinella, Hastigerinopsis.
    - Family OrbulinidaeSchultze 1854, genera Biorbulina, Candorbulina, Orbulina, Praeorbulina.
    - Family SphaeroidinellidaeBanner & Blow 1959, genera Prosphaeroidinella, Sphaeroidinella, Sphaeroidinellopsis.
    - Family TurborotalitidaeHofker 1976, genera Berggrenia, Turborotalita.
  - Superfamily GloborotalioideaCushman 1927
    - †Family CatapsydracidaeBolli, Loeblich & Tappan 1957, genera Catapsydrax, Globigerinopsoides, Globigerinoita, Velapertina.
    - Family GloborotaloididaeBanner & Blow 1959, genera Clavatorella, Globorotaloides, Protentelloides.
    - Family GloborotaliidaeCushman 1927, genera Dentigloborotalia, Globoconella, Globorotalia, Hirsutella, Jenkinsella, Menardella, Neogloboquadrina, Paragloborotalia, Truncorotalia.
    - Family PulleniatinidaeCushman 1927, genus Pulleniatina.
  - †Superfamily GlobanomalinidoideaLoeblich & Tappan 1984, family GlobanomalinidaeLoeblich & Tappan 1984, genera Carinoturborotalia, Globanomalina, Luterbacheria, Planoglobanomalina, Turborotalia.
  - †Superfamily HantkeninoideaCushman 1927
    - †Family PseudohastigerinidaeCanudo 1990, genus Pseudohastigerina.
    - †Family HantkeninidaeCushman 1927, genera Applinella, Aragonella, Clavigerinella, Cribrohantkenina, Hantkenina.
  - †Superfamily TruncorotaloidinoideaBouDagher-Fadel 2012
    - †Family GlobigerapsidaeBlow 1979, genera Globigerapsis, Muricoglobigerina.
    - †Family PlanorotalitidaeBouDagher-Fadel 2012, genera Astrorotalia, Planorotalites.
    - †Family TruncorotaloididaeLoeblich & Tappan 1961. Acarinina, Igorina, Morozovella, Morozovelloides, Pearsonites, Praemurica, Pseudogloboquadrina, Testacarinata, Truncorotaloides.
- †Order GlobotruncanidaArz, Arenillas & Gilabert 2022^[180]
  - †Superfamily AbathomphaloideaArz, Arenillas & Gilabert 2022
    - †Family AbathomphalidaePessagno 1967, genus Abathomphalus.
    - †Family GlobotruncanellidaeMaslakova 1964, genera Globotruncanella, Spinoglobotruncanella.
  - †Superfamily FavuselloideaLongoria 1974
    - †Family ConoglobigerinidaeBouDagher-Fadel, Banner & Whittaker 1997, genera Conoglobigerina, Tenuigerina, ^?Sphaerogerina.
    - †Family FavusellidaeLongoria 1974, genera Ascoliella, Favusella, Koutsoukosia.
    - †Family GlobuligerinidaeLoeblich & Tappan 1984, genera Compactogerina, Globuligerina, Haeuslerina, Petaloglobigerina.
  - †Superfamily HedbergelloideaLongoria & Gamper 1975
    - †Family AnaniidaeEl-Nakhal 2010, genera Anania, Badriella, Costellagerina, Hillsella, Liuenella [Liuella], Loeblichella, Muricohedbergella, Paracostellagerina, Pessagnoina, Planohedbergella, Pseudoclavihedbergella, Vanhintella.
    - †Family HedbergellidaeLoeblich & Tappan 1961, genera Asterohedbergella, Clavihedbergella, Hedbergella, Microhedbergella, Paraticinella, Pseudoguembelitria.
    - †Family HelvetoglobotruncanidaeLamolda 1976, genera Angulocarinella, Bermudeziana, Bollitruncana, Fingeria, Hedbergellita, Brittonella, Helvetoglobotruncana, Unitruncatus, Whiteinella.
    - †Family PraehedbergellidaeBanner & Desai 1988, genera Blefuscuiana, Gorbachikella, Praehedbergella, Lilliputianella, Lilliputianelloides, Wondersella.
  - †Superfamily GlobotruncanoideaBrotzen 1942
    - †Family GlobotruncanidaeBrotzen 1942, genera Contusotruncana, Globotruncana, Marginotruncana, Obliquacarinata, Sphaerotruncana, Ventrotruncana.
    - †Family PraeglobotruncanidaeIon 1983, genera Concavatotruncana, Dicarinella, Falsotruncana, Rotundina, Praeglobotruncana, Verotruncana.
    - †Family ReissidaeKorchagin 2001, genera Elevatotruncana, Globotruncanita, Kassabiana, Radotruncana, Sigalitruncana, Turbotruncana.
  - †Superfamily PlanomalinoideaBolli, Loeblich & Tappan 1957
    - †Family EohastigerinellidaeLoeblich & Tappan 1984, genera Eohastigerinella, Hastigerinoides.
    - †Family GlobigerinelloididaeLongoria 1974, genera Alanlordella, Allotheca, Biglobigerinella, Blowiella, Claviblowiella, Globigerinelloides, Pseudoschackoina.
    - †Family PlanomalinidaeBolli, Loeblich & Tappan 1957, genera Bannerina, Planomalina, Pseudoplanomalina.
    - †Family SchackoinidaePokorný 1958, genera Asymetria, Groshenyia, Leupoldina, Neoschackoina, Schackoina.
  - †Superfamily RotaliporoideaSigal 1958
    - †Family RotaliporidaeSigal 1958, genera Anaticinella, Pseudothalmanninella, Rotalipora, Thalmanninella.
    - †Family TicinellidaeLongoria 1974, genera Biticinella, Claviticinella, Ticinella.
  - †Superfamily RugoglobigerinoideaSubbotina 1959
    - †Family HelvetiellidaeLongoria & Gamper 1984, genera Archaeoglobigerina, Bucherina, Dorbignya, Edgarinella, Gandolfia, Gansserina, Globocarinata, Helvetiella, Kuglerina.
    - †Family RugoglobigerinidaeSubbotina 1959, genera Archaeoglobitruncana, Plummerita, Rugoglobigerina, Rugosocarinata, Rugotruncana, Trinitella.
- †Order HeterohelicidaFursenko 1958 emend. Arz, Arenillas & Gilabert 2022^[180]
  - †Superfamily HeterohelicoideaCushman 1927
    - †Family GublerinidaeAliyulla 1977, genera Gublerina, Lipsonia, Praegublerina.
    - †Family HeterohelicidaeCushman 1927, genera Braunella, Bronnimannella, Ehrenbergites, Globoheterohelix, Fleisherites, Hartella, Heterohelix, Huberella, Laeviheterohelix, Lazarusina, Lunatriella, Magellanina, Mihaia, Nederbragtina, Planoheterohelix, Protoheterohelix, Pseudoplanoglobulina, Steineckia, Striataella, Texasina, ^?Bifarina, ^?Rectoguembelina, ^?Zeauvigerina.
    - †Family PseudotextulariidaeMaamouri & Salaj 1978, genera Planoglobulina, Pseudotextularia, Racemiguembelina.
    - †Family PseudoguembelinidaeAliyulla 1977, genera Eicheriella, Leptobimodalia, Pseudoguembelina.
    - †Family SpiroplectidaeCushman 1911, genera Hendersonites (=Hendersonia), Neohendersonites, Paraspiroplecta, Spiroplecta.
    - †Family VentilabrellidaeMaamouri & Salaj 1978, genera Planulitella, Proliferania, Sigalia, Ventilabrella.
- †Order GuembelitriidaArenillas, Arz & Gilabert 2022^[180]
  - †Superfamiily CassigerinelloideaBolli, Loeblich & Tappan 1957, family CassigerinellidaeBolli, Loeblich & Tappan 1957, genera Cassigerinella, Riveroinella.
  - †Superfamily GuembelitrioideaMontanaro-Gallitelli 1957, family GuembelitriidaeMontanaro-Gallitelli 1957, genera Cassigerinelloita, Guembelitria, Chiloguembelitria, Jenkinsina, ?Archaeoguembelitria, ?Gallitellia, ?Guembelitriella.
  - †Superfamily ChiloguembelinoideaReiss 1963, family ChiloguembelinidaeReiss 1963, genera Chiloguembelina, Woodringina, ?Streptochilus.
  - †Superfamily GloboconusoideaBouDagher-Fadel 2012, family GloboconusidaeBouDagher-Fadel 2012, genera Globoconusa, Trochoguembelitria,
- Order ? (unnamed)^[180]
  - Superfamily GlobigerinitoideaBouDagher-Fadel 2012, emend. Arenillas, Arz & Gilabert 2022^[180]
    - Family CandeinidaeCushman 1927. Candeina.
    - †Family GlobigerinatellidaeBouDagher-Fadel 2012. Globigerinatella.
    - Family GlobigerinitidaeBermúdez 1961, genera Globigerinita, Mutabella, Polyperibola, Tinophodella.
    - Family TenuitellidaeBouDagher-Fadel 2012, genera Praetenuitella, Tenuitella, Tenuitellinata, Tenuitellita.
    - †Family ? (unnamed), genera Dipsidripella, ?Antarcticella.
- Order RobertinidaLoeblich & Tappan 1984, genera Hoeglundina, Robertina, Robertinoides.
- Order Textulariida^(P)Delage & Hérouard 1896, genera Cyclammina, Eggerella, Reophax, Textularia, Trochammina.
- Order CarterinidaLoeblich & Tappan 1981, genus Carterina.

Radiolaria

RadiolariaMüller 1858, sensu Adl et al. 2005
- AcanthareaHaeckel 1881, emend. Mikrjukov 2000
  - ChaunocanthidaSchewiakoff 1926. Amphiacon, Conacon, Gigartacon, Heteracon, Stauracon.
  - HolocanthidaSchewiakoff 1926. Acanthochiasma, Acanthocolla, Acanthoplegma.
  - SymphyacanthidaSchewiakoff 1926. Amphilithium, Astrolonche, Pseudolithium.
  - ArthracanthidaSchewiakoff 1926. Acanthometra, Daurataspis, Dictyacantha, Diploconus, Phractopelta, Phyllostaurus, Pleuraspis, Stauracantha.
- TaxopodidaFol 1883. Sticholonche.
- PolycystineaEhrenberg 1839 stat. nov. Levine et al. 1980^[198]
  - SpumellariaEhrenberg 1876 stat. nov. Haeckel 1884
    - HexacromyoideaHaeckel 1882 stat. nov. Suzuki et al. 2021 [Hexalonchata Afanasieva et al. 2005]
      - HexacaryidaeHaeckel 1882 stat. nov. Suzuki et al. 2021: ClevepilegmaDumatrica 2013, HaliphormisEhrenberg 1846 [Hexastylanthus, Hexastylettus; Hexastylissus; Hexastylurus], HexacaryumHaeckel 1882, HexalonchettaHaeckel 1887, HexancistraHaeckel 1879 [Hexancora], HexapitysHaeckel 1882.
      - HexacromyidaeHaeckel 1882 stat. nov. Suzuki et al. 2021: CarpocanthumChen & Tan 1989, HexacromyumHaeckel 1882 [Cubosphaera; Hexacontura], HexalonchillaHaeckel 1887 [Hexalonchusa; Staurolonchantha], NaninaKozur & Mostler 1982 [Pentactinosphaera].
      - HollandosphaeridaeDeflandre 1973: AnomalosomaLoeblich & Tappan 1961 [HeterosomaHollande & Enjumet 1960, HollandosphaeraDeflandre 1973 [HeliasterHollande & Enjumet 1960], TetrapetalonHollande & Enjumet 1960.
    - SpongosphaeroideaHaeckel 1862 → SpongosphaeridaeHaeckel 1862: DiplospongusMast 1910, SpongodendronHollande & Enjumet 1960, SpongosphaeraEhrenberg 1847 [Hexadoridium; Spongosphaeromma].
    - LithocyclioideaEhrenberg 1846
      - AstracturidaeHaeckel 1882: AstrommaEhrenberg 1846 [Astractinium; Astractura; Astracturium; Astrococcura; Staurococcura], AmphacturaHaeckel 1882 [Dicoccura; Diplactinium], HymeniastrumEhrenberg 1846 [Hymenastrella; Hymenactura; Hymenacturium; Trigonactinium; Hymenactinium; Pentactura; Trigonacturium].
      - LithocycliidaeEhrenberg 1846: CromyatractusHaeckel 1887 [Cromyatractium; Caryatractus], HeliosestrumHaeckel 1882 [Heliosestantha; Astrosestrum; Astrosestantha; Astrophacura; StaurodiscusKrasheninnikov 1960]; HeliostylusHaeckel 1882 [Astrostylus; Stylodiscus; Stylentodiscus], LithocycliaEhrenberg 1846 [Astrocyclia; Coccodiscus], PhacostaurusHaeckel 1882 [Phacostaurium, Astrostaurus, Crucidiscus, Heliostaurus, Sethostaurium, Sethostaurus, Staurentodiscus], PhacotriactisSutton 1896, SethostylusHaeckel 1882 [Sethostylium; Amphicyclia; Phacostylus; Phacostylium], StaurocycliaHaeckel 1882 [Coccostaurus], TriactiscusHaeckel 1882 [Trigonocyclia].
      - PanartidaeHaeckel 1887: CannartusHaeckel 1882 [Cannartidissa; Cannartiscus; Pipetta; Pipettaria; Pipettella; Druppula; Druppuletta], DiartusSanfilippo & Riedel 1980, DidymocyrtisHaeckel 1862 [Artidium; Cyphinura; Cyphocolpus; Desmartus; Ommatocampula; Panaromium; Panartus; Panartella; Panartidium; Panartissa; Panartura; Peripanartium; Peripanartula; Peripanartus; Peripanicula], SpongolivellaDumitrica 2021.
      - PhacodiscidaeHaeckel 1882: PeriphaenaEhrenberg 1874 [Astrophacomma; Heliodiscomma; Perizona], PhacodiscusHaeckel 1882 [Phacodiscinus; Astrophacilla; Paracenodiscus; Phacodisculus; Prunulum; Prunuletta; Sethodiscinus].
    - SpongodiscoideaHaeckel 1862 emend. Suzuki 2021
      - SpongodiscidaeHaeckel 1862: SpongasterEhrenberg 1861 [Spongastrella; Histiastrella], SpongodiscusEhrenberg 1854 [Spongodisculus], SpongotrochusHaeckel 1861 [Spongotrochiscus].
      - EuchitoniidaeStöhr 1880 emend. Suzuki 2021: AmphicraspedumHaeckel 1882 [Amphicraspedon; Aphirrhopella], DictyocoryneEhrenberg 1861 [Dictyocorynula; Dictyastrum; Dictyastrella; Euchitonia; Hymenastromma; Rhopalodictya; Rhopalodictyum; Styla; Pteractis], HexinastrumHaeckel 1882 [Hexalastromma; Pentalastromma; Pentinastrum], OmmatocampeHaeckel 1861 [Ommatocampium; Amphymenium], TessarastrumHaeckel 1887 [Tessarastrella; Hagiastromma; Tessarostromma], TricanastrumHaeckel 1879 [Dicranaster; Dicranastrum; Myelastrella; Myelastrum; Spongomyelastrum; Myelastromma; Pentophiastromma; Spongodicranastrum; Spongohagiastrum; Spongopentophiastrum; Spongostaurina; Tetracranastrum; Triastrum], TrigonastrumHaeckel 1887 [Trigonastrella; Rhopalastromma; Chitonastromma; Amphicraspedina; Amphirrhopoma; Dictyastromma; Monaxonium; Trigonastromma].
      - SpongobrachiidaeHaeckel 1882 emend. Suzuki 2021: SpongasteriscusHaeckel 1862 [Spongasterisculus; Dictyocorynium], SpongastrommaHaeckel 1887, SpongobrachiumHaeckel 1882.
    - CladococcoideaHaeckel 1862 stat. nov. Suzuki et al. 2021
      - EthmosphaeridaeHaeckel 1862: CyrtidosphaeraHaeckel 1861, EthmosphaeraHaeckel 1861, [Ethmosphaerella; Monosphaera], HaplosphaeraHollande & Enjumet 1960, HeliosphaeraHaeckel 1861 [Heliosphaerella], LiosphaeraHaeckel 1887 [Melitomma, Craspedomma].
      - CladococcidaeHaeckel 1862: ArachnosphaeraHaeckel 1861 [Arachnosphaerella], ArachnospongusMast 1910, CladococcusMüller 1856 [Cladococcalis; Anomalacantha; Cladococcodes; Cladococcurus; Porococcus], DiplosphaeraHaeckel 1861 [Diplosphaeromma; Astrosphaera; Diplosphaerella; Leptosphaera; Leptosphaerella; Astrosphaerella; Astrospongus; Drymosphaeromma; Leptosphaeromma], HaeckeliellaHollande & Enjumet 1960, LychnosphaeraHaeckel 1882 [Rhizoplegmidium, Rhizospongus, Thalassoplegma].
    - TrematodiscoideaHaeckel 1862 emend. Suzuki 2021 → TrematodiscidaeHaeckel 1862 emend. Suzuki 2021: FlustrellaEhrenberg 1839 [Centrospira; Discospirella; Trematodiscus; Perichlamydium; Perispirella; Stylochlamyum], StaurospiraHaeckel 1887 [Staurodictyon; Tholodiscus; Xiphospira], StylodictyaEhrenberg 1846 [Stylodictyon; Stylochlamydium; Stylochlamys; Stylospongia; Stylocyclia; Stylospira], TripodictyaHaeckel 1882 [Xiphodictyon].
    - HaliommoideaEhrenberg 1846
      - ActinommidaeHaeckel 1862 emend. Suzuki 2021: ActinommaHaeckel 1861 [Actinommetta; Haliommura; Rhaphidococcus; Riedelipyle; Dreyerella; Drymyomma; Cromyomma; Echinommura; Heliosomura; Spheropyle], CromyechinusHaeckel 1882 [Cromyodrymus], RhaphidocapsaHaeckel 1887, SphaeractisBrandt in Wetzel 1936, StaurocaryumHaeckel 1882, StomatosphaeraDreyer 1889, StuermeriaDeflandre 1964.
      - HaliommidaeEhrenberg 1846 emend. Suzuki 2021: CromyosphaeraHaeckel 1882 [Cromyommetta; Cromyommura], HaliommaEhrenberg 1839 [Actinommilla; Cenosphaera; Circosphaera; Thecosphaerella], HaliommanthaHaeckel 1887, HexacontellaHaeckel 1887, MelittosphaeraHaeckel 1882 [Conoactinomma], PseudostaurosphaeraKrasheninnikov 1960 [Pseudostaurolonche].
      - HeliodiscidaeHaeckel 1882 sensu De Wever et al. 2001: ActinommuraHaeckel 1887 [Excentrosphaerella], ExcentrococcusDumitrica 1978, ExcentrodiscusHollande & Enjumet 1960, HeliodiscusHaeckel 1862 [Heliodiscilla, Heliocladus, Heliodiscetta, Heliodrymus, Heliodendrum, Heliosestilla], HelioferrusaDumitrica 2019, PhaenicosphaeraHaeckel 1887 [Dreyeropyle].
    - LithelioideaHaeckel 1862 sensu Matsuzaki et al. 2015
      - †ConocaryommidaeLipman 1969: ConocaryommaLipman 1969 [Conocromyomma].
      - LitheliidaeHaeckel 1862 emend. Suzuki 2021: LitheliusHaeckel 1861 [Lithospira; Azerbaidjanicus], MiddouriumKozlova 1999 [Monobrachium], SpiremariaKozlova 1960 [Spiromultitunica], SpongocycliaHaeckel 1862 [Lithocarpium; Ommatodiscinus; Ommatodiscus; Ommatodisculus].
      - †PhaseliformidaePessagno 1972: PhaseliformaPessagno 1972.
      - †PyramispongiidaeKozur & Mostler 1978 sensu O'Dogherty 1994: PyramispongiaPessagno 1973 [Nodotetraedra].
      - SponguridaeHaeckel 1862: OmmatogrammaEhrenberg 1861 [Spongurus; Spongocorisca; Spongurantha; Spongurella].
    - SpongopyloideaDreyer 1889 emend. Suzuki 2021
      - SpongopylidaeDreyer 1889 emend. Suzuki 2021: SchizodiscusDogiel in Dogiel & Reshetnyak 1952, SpongobrachiopyleKozur & Mostler 1978, SpongopyleDreyer 1889 [Spongopylarium], SpongospiraStöhr 1880.
      - CristallosphaeridaePopofsky 1912: CalcarommaThomson 1877 [Cristallosphaera], EnalomelonSugiyama 1992.
      - PrunopylidaePoche 1913: PrunopyleDreyer 1889, SpongopylidiumDreyer 1889.
    - PhorticioideaHaeckel 1882 stat. nov. Suzuki et al. 2021 [Larnacillilae De Wever et al. 2001]
      - AmphitholidaeHaeckel 1887 stat. nov. sensu De Wever et al. 2001
      - CircodiscidaeDumitrica 1989 stat. nov. Suzuki et al. 2021
      - CryptolarnaciidaeDumitrica 1989 stat. nov. Suzuki et al. 2021
      - HistiastridaeDumitrica 1989 stat. nov. Suzuki et al. 2021
      - PhorticiidaeHaeckel 1882 sensu Dumitrica 1989
    - LarcospiroideaHaeckel 1887 stat. nov. sensu Dumitrica 1989
      - DipylissidaeDumitrica 1989 stat. nov. Suzuki et al. 2021
      - LarcospiridaeHaeckel 1887 stat. nov. Suzuki et al. 2021
      - PalaeotetrapylidaeDumitrica 1989 stat. nov. Suzuki et al. 2021
      - PylodiscidaeHaeckel 1887 sensu Dumitrica 1989
      - ZonariidaeHaeckel 1887 sensu Dumitrica 1989
    - PseudoaulophacoideaRiedel 1967 sensu De Wever et al. 2001
      - PatulibracchiidaePessagno 1971 sensu De Wever et al. 2001
      - PseudoaulophacidaeRiedel 1967 sensu De Wever et al. 2001
      - SuttoniidaeSchaaf 1976 sensu Dumitrica 2019
    - StylosphaeroideaHaeckel 1887 sensu Dumitrica 1984
      - EntapiidaeDumitrica in De Wever, Dumitrica, Caulet Nigrini & Caridroit 2001
      - StylatractidaeSchröder 1909 emend. Suzuki 2021
      - TubosphaeridaeSuzuki 2021
  - NassellariaEhrenberg 1875 emend. Haeckel 1887. Artostrobus, Eucyrtidium, Lithomelissa, Pterocanium, Pterocorys.
  - CollodariaHaeckel 1887. Acrosphaera, Collosphaera, Collozoum, Sphaerozoum, Rhaphidozoum, Siphonsphaera, Thalassicolla.
  - OrodariaNakamura & Suzuki 2020^[199]
    - OroscenidaeHaeckel 1887 emend. Nakamura & Suzuki 2021 [Orosphaerida Haeckel 1887; Orosphaeridae Haecker 1908]. Oroscena, Orostaurus, Oropelex. Nomina dubia genera: Orosphaera, Orodictyum, Orona, Oronium.
    - ThalassothamnidaeHaecker 1906 emend. Nakamura & Suzuki 2021 [Cytocladidae Schröder, 1908]. Thalassothamnus, Cytocladus. Nomen dubium genus: Conostylus.
  - †EntactinariaKozur & Mostler 1982 sensu Nakamura & Suzuki 2020^[s]
    - †EntactiniidaeRiedel 1967. Afanasievella, Apophysiactinia, Borisella, Callela, Cancellosphaera, Costaentactinia, Cyclocarpusnomen dubium, Duodecimentactinia, Langsonsphaera,^[200]Entactinosphaera, Gracilentactinia, Holdisphaera, Involutentactinia, Kashiwara, Magnentactinia, Magnisphaera, Microporosa, Moskovistella, Multientactinia, Munzuwonella, Paratriposphaera, Perforentactinia, Plenoentactinia, Plenosphaera, Pluristratoentactinia, Polyedroentactinia, Provisocyntra, Radiobisphaera, Retentactinia, Retisphaera, Sinosphaera, Spongentactinia, Stigmosphaerostylus, Trilonche, Uberinterna, Wuyia.^[201]
    - †TetrentactiniidaeKozur & Mostler 1979. Multisphaera.
    - †TriassothamnidaeTakahashi, Maekawa & Dumitrica 2022. Triassothamnus.^[200]

Disparia

Disparia is a clade that unites several predatory protists, namely the provorans, hemimastigotes, and two mysterious genera Meteora and Solarion. It was described in 2025 through phylogenomic analyses that accompanied the discovery of Solarion.^[202] Prior to these analyses, provorans, hemimastigotes and Meteora were considered 'orphan' taxa, with unstable phylogenetic positions. The first provoran, Ancoracysta twista, was briefly proposed to be related to Haptista.^[203] However, in 2024 there was already evidence of a close affinity between Meteora, hemimastigotes, and provorans.^[204] The phylum Caelestes, described in 2025, encompasses two monotypic genera of protists with a unique stalked extrusome used for immobilizing prey bacteria. Their morphology resembles that of celestial bodies, after which they are named. Only one of the genera, Solarion, is assigned to a family, and no classes or orders have been defined.^[202] Hemimastigotes are a small group composed of ten species of heterotrophs with a pellicle and numerous flagella. First identified in 1988,^[205] they remained an orphan group for decades due to the absence of genetic information, with taxonomists hypothesizing affinities to many different protists.^[206] In 2018, two hemimastigotes were successfully sequenced and a phylogenomic analysis revealed their deep-branching placement near Diaphoretickes.^[207] Between 2024 and 2025, a closer relationship with the clades Provora and Caelestes was resolved.^[204]^[202] Provorans compose two ancient phyla of predatory microbes and a total of eight described species. They are small, fast-swimming predators capable of consuming larger prey, but are easily confused with other protists due to their unremarkable appearance; they required meticulous study to be recognized.^[208]^[209]^[210]

ProvoraTikhonenkov et al. 2022
- Phylum NebulidiaTikhonenkov et al. 2022, class NebulideaTikhonenkov et al. 2022, order NebulididaTikhonenkov et al. 2022, family NebulidaeTikhonenkov et al. 2022, genera Ancoracysta, Nebulomonas.
- Phylum NibbleridiaTikhonenkov et al. 2022, class NibblerideaTikhonenkov et al. 2022, order NibblerididaTikhonenkov et al. 2022, family NibbleridaeTikhonenkov et al. 2022, genera Nibbleromonas, Ubysseya.
MembriferaValt & Čepička in Valt et al. 2025
- Phylum CaelestesValt & Čepička in Valt et al. 2025
  - MeteoraHausmann, Weitere, Wolf & Arndt 2002
  - Family SolarionidaeValt & Čepička in Valt et al. 2025, sole genus Solarion.
- Phylum HemimastigophoraFoissner, Blatterer & Foissner 1988, class HemimastigeaFoissner, Blatterer & Foissner 1988, order HemimastigidaFoissner, Blatterer & Foissner 1988.
  - Family SpironematellidaeSilva 1980 emend. Shɨshkin 2022, genera Hemimastix, Spironematella (="Spironema"),^[211]Stereonema.
  - Family ParamastigidaeSkuja 1948 emend. Karpov 2012, genus Paramastix.

Excavates

Malawimonadida

MalawimonadidaeO' Kelly & Nerad 1999. Gefionella, Malawimonas.
ImasidaeHeiss, Simpson, & Kim 2020. Imasa.^[212]

Metamonada

The metamonads were first described by Pierre-Paul Grassé in the first volume of Traité de Zoologie, published in 1952, as the superorder Metamonadina or Anaxostylaria. They were originally composed of zooflagellates with four or more flagella, known as polymastigotes and hypermastigotes (e.g., Trichomonas, Oxymonas).^[213] These were later split into other groups such as the Parabasalia and Preaxostyla (over 260 and 140 species respectively),^[214]^[215] regarded as individual phyla. After rRNA phylogenetic analyses demonstrated their relatedness, the concept of metamonads was reintroduced by Cavalier-Smith as a monophyletic phylum Metamonada that includes both groups, as well as the anaerobic Fornicata (e.g., the free-living Carpediemonas and the parasitic Giardia;^[216]^[217] around 140 species).^[214] In this system, Preaxostyla is known as subphylum Anaeromonada, and Fornicata and Parabasalia are two infraphyla that belong to the subphylum Trichozoa.^[11] Still, some taxonomists retain the Parabasalia at a phylum level.^[218]

The classifications of Preaxostyla and Fornicata were last revised separately in the 2017 Handbook of the protists^[219]^[220]^[221] and the higher classification of Metamonada was revised by Cavalier-Smith in 2021.^[11] The classification of Parabasalia was completely updated in 2024.^[218] Two new smaller clades of metamonads have been described in addition: anaeramoebae^[222] and the 'BaSk' clade, containing barthelonids and skoliomonads.^[223] However, Parabasalia was treated as a separate phylum by the 2024 revision, instead of a member of phylum Metamonada.^[218]

Phylum MetamonadaGrassé 1952 emend.stat. n. Cavalier-Smith 2003

Family AnaeramoebidaeTáborský, Pánek & Čepička 2017, genus Anaeramoeba.
Subphylum Anaeromonada (=Preaxostyla Simpson 2003), class AnaeromonadeaCavalier-Smith 1996 emend. 2003
- Order TrimastigidaCavalier-Smith 2003 emend. 2021, family TrimastigidaeKent 1880 emend. Zhang et al. 2015, genus Trimastix.
- Order ParatrimastigidaCavalier-Smith 2022, family ParatrimastigidaeZhang, Taborsky, Silberman, Panek, Čepička & Simpson 2015, genus Paratrimastix.
- Order OxymonadidaGrassé 1952. Genus not assigned to any family: Opisthomitus.^[t]
  - Family Oxymonadidae, genera Barroella, Oxymonas, Microrhopalodina, Sauromonas, †Oxymonites, †Microrhopalodites, †Sauromonites.
  - Family Polymastigidae, genera Blattamonas, Brachymonas, Monocercomonoides, Paranotila, Polymastix, Tubulimonoides.
  - Family Pyrsonymphidae, genera Dinenympha, Pyrsonympha, †Dinenymphites, †Pyrsonymphites.
  - Family Saccinobaculidae, genera Notila, Saccinobaculus.
  - Family Streblomastigidae, genus Streblomastix.
Subphylum Trichozoa^(P)^[224]Cavalier-Smith 1997
- Infraphylum FornicataSimpson 2003 stat. n. Cavalier-Smith 2022. Genus not assigned to any lower taxon: Aduncisulcus.
  - Class Carpomonadea^(P)Cavalier-Smith 2013
    - Order Carpediemonadida^(P)Cavalier-Smith 2013
      - Family Carpediemonadidae^(P)^[224]Cavalier-Smith 2013, genera Carpediemonas, Hicanonectes, Ergobibamus.
      - Family KipferliidaeCavalier-Smith 2013, genus Kipferlia.
    - Order Chilomastigida^(P)^[225]Cavalier-Smith 2013, family Chilomastigidae^(P)^[225]Cavalier-Smith 2013, genus Chilomastix^(P)^[225].
    - Order DysnectidaCavalier-Smith 2013, family DysnectidaeCavalier-Smith 2013, genus Dysnectes.
  - Class Eopharyngea^(P)^[226]Cavalier-Smith 1993 stat. n. 2013
    - Family CaviomonadidaeCavalier-Smith 2013, genera Caviomonas, Iotanema, Euthynema^[227].
    - Order Retortamonadida^(P)^[225]^[u]Grassé 1952 emend. Cavalier-Smith 2013, family Retortamonadidae^(P)^[231]Wenrich 1932, genus Retortamonas^(P)^[232].
    - Order DiplomonadidaWenyon 1926 (=Diplozoa Dangeard 1910)
      - Suborder DistomatinaKent 1880 (=Hexamitinae Kent 1880). Genera not assigned to any lower taxon: Gyromonas, Trigonomonas.
        Family SpironucleidaeCavalier-Smith1996, genus Spironucleus.
        Family EnteromonadidaeKulda and Nohynková 1976, genus Enteromonas.
        Family Hexamitidae^(P)^[225]Kent 1881, genera Trepomonas, Hexamita, Trimitus.
      - Suborder GiardiinaKulda & Nohýnková 1978 (=Giardiinae Kulda & Nohýnková 1978)
        Family Octomitidae^(P?)Cavalier-Smith 1996, genera Octomitus, Brugerolleia.
        Family GiardiidaeCavalier-Smith 1996, genus Giardia.
- Infraphylum ParabasaliaHonigberg 1973. Genera incertae sedis: Chilomitus, Rhizonympha, Tricercomitus, Trichocovina.
  - Class HypotrichomonadeaČepička, Hampl & Kulda 2010, order HypotrichomonadidaČepička, Hampl & Kulda 2010, family HypotrichomonadidaeHonigberg 1963 emend. Čepička, Hampl & Kulda 2010, genera Hypotrichomonas, Trichomitus.
  - Class PimpavickeaBoscaro & Keeling 2024, order PimpavickidaCéza & Čepička 2022, family PimpavickidaeCéza & Čepička 2022, genera Pimpavicka, Alexandriella.
  - Class TrichomonadeaKirby 1947 sensu Čepička, Hampl & Kulda 2010
    - Order HonigbergiellidaČepička, Hampl & Kulda 2010 emend. Boscaro & Keeling 2024
      - Family HexamastigidaeČepička, Hampl & Kulda 2010 emend. Boscaro & Keeling 2024, genus Hexamastix.
      - Family HonigbergiellidaeČepička, Hampl & Kulda 2010, genera Honigbergiella, Ditrichomonoides, Honigbergiellopsis, Monotrichomonas.
      - Family CthulhuidaeBoscaro & Keeling 2024, genera Cthulhu, Cthylla, Nyarlathotep.
      - Family TetratrichomastigidaeBoscaro & Keeling 2024, genus Tetratrichomastix.
    - Order TrichomonadidaKirby 1947 sensu Čepička, Hampl & Kuda 2010. Genera incertae sedis: Pseudotrichomonas, †Paleotrichomones.^[233]
      - Family LacusteriidaeCéza & Čepička 2022, genus Lacusteria.
      - Family TrichomonadidaeChalmers & Pekkola 1918 sensu Hampl, Vrlík, Čepička, Pecka, Kulda & Tachezy 2006, genera Trichomonas, Cochlosoma, Cyathosoma, Pentatrichomonas, Pentatrichomonoides, Pseudotrypanosoma, Ptychostoma, Tetratrichomonas, Trichomitopsis, Trichomonoides.
  - Clade "Tla"
    - Class LophomonadeaBoscaro & Keeling 2024, order LophomonadidaLight 1927 emend. Cavalier-Smith 2013, family LophomonadidaeKent 1880 emend. Cavalier-Smith 2013, genera Lophomonas, Eulophomonas, Prolophomonas.
    - Class TrichonympheaPoche 1913, order TrichonymphidaPoche 1913
      - †Family BurmanymphidaePoinar 2009, genus Burmanympha.^[233]
      - Family BarbulanymphidaeBoscaro & Keeling 2024, genera Barbulanympha, Rhynchonympha, Urinympha.
      - Family HoplonymphidaeLight 1926 emend. Boscaro & Keeling 2024, genus Hoplonympha.
      - Family RetractinymphidaeRadek & Brune 2023, genus Retractinympha.
      - Family SpirotrichosomidaeHollande & Carruette-Valentin 1971, genera Spirotrichosoma, Apospironympha, Bispironympha, Colospironympha, Heliconympha, Leptospironympha, Macrospironympha.
      - Family StaurojoeninidaeGrassi 1917, genera Staurojoenina, Idionympha.
      - Family TeranymphidaeKoidzumi 1921, genera Tetranympha, Eucomonympha, Pseudotrichonympha.
      - Family TrichonymphidaeKent 1880, genus Trichonympha.
  - Clade "Cadamassta"
    - Class CristamonadeaČepička, Hampl & Kulda 2010. Genera incertae sedis: Cyclojoenia, Joenia, Joenina, Joenoides, Joenopsis, Pachyjoenia, Parajoenopsis, Placojoenia, Projoenia.
      - Order CalonymphidaBoscaro & Keeling 2024
        Family CalonymphidaeGrassi 1911 sensu Gile 2011, genera Calonympha, Criconympha, Daimonympha, Diplonympha, Gyronympha, Metastephanonympha, Prosnyderella, Snyderella, Stephanonympha.
        Family DeltotrichonymphidaeBrugerolle & Lee 2000, genera Deltotrichonympha, Koruga.
        Family MixotrichidaeBoscaro & Keeling 2024, genus Mixotricha.
      - Order DevescovinidaBoscaro & Keeling 2024, family DevescovinidaeDoflein 1911 emend. Boscaro & Keeling 2024, genera Devescovina, Achemon, Astronympha, Bullanympha, Caduceia, Coronympha, Evemonia, Foaina, Hyperdevescovina, Kirbynia, Kofoidia, Macrotrichomonas, Macrotrichomonoides, Metadevescovina, Parajoenia, Polymastigoides, Pseudodevescovina, Runanympha, †Devescovites.^[233]
      - Order GigantomonadidaBoscaro & Keeling 2024, family GigantomonadidaeBoscaro & Keeling 2024, genus Gigantomonas.
    - Class DientamoebeaBoscaro & Keeling 2024, order DientamoebidaBoscaro & Keeling 2024, family DientamoebidaeGrassé 1953, genera Dientamoeba, Histomonas, Parahistomonas, Protrichomonas.
    - Class MonocercomonadeaBoscaro & Keeling 2024, order MonocercomonadidaBoscaro & Keeling 2024, family MonocercomonadidaeKirby 1944, genus Monocercomonas.
    - Class SimplicimonadeaBoscaro & Keeling 2024, order SimplicimonadidaBoscaro & Keeling 2024, family SimplicimonadidaeČepička, Hampl & Kulda 2010, genus Simplicimonas.
    - Class TritrichomonadeaČepička, Hampl & Kulda 2010 emend. Boscaro & Keeling 2024, order TritrichomonadidaČepička, Hampl & Kulda 2010 emend. Boscaro & Keeling 2024, family TritrichomonadidaeČepička, Hampl & Kulda 2010, genus Tritrichomonas.
    - Class SpirotrichonympheaGrassé 1952 sensu Čepička, Hampl & Kulda 2010
      - Order CononymphidaBoscaro & Keeling 2024, family CononymphidaeBoscaro & Keeling 2024, genus Cononympha.
      - Order HolomastigotoididaBoscaro & Keeling 2024, family HolomastigotoididaeGrassi & Foà 1911, genera Holomastigotoides, Rostronympha.
      - Order SpirotrichonymphidaGrassé 1952
        Family BrugerollinidaeBoscaro & Keeling 2024, genera Brugerollina, Pseudospironympha.
        Family FraterculidaeBoscaro & Keeling 2024, genera Fraterculus, Cuppa.
        Family HolomastigotidaeJanicki 1915, genera Holomastigotes, Spiromastigotes, Spirotrichonymphella, Uteronympha.
        Family SpirotrichonymphidaeGrassi 1917, genera Spirotrichonympha, Microjoenia, Micromastigotes, Nanospironympha, Spironympha, Torquenympha.
Incertae sedis
- Class NotopharyngeaShiratori et al. 2026 (=BaSk Williams et al. 2024^[234])^[235]
  - Order BarthelonidaShiratori et al. 2026, family BarthelonidaeShiratori et al. 2026, genera Barthelona, Microbarthelona, Parabarthelona.
  - Order SkoliomonadidaShiratori, Eglit, Yazaki, Inagaki & Simpson 2026, family SkoliomonadidaeShiratori, Eglit, Yazaki, Inagaki & Simpson 2026, genus Skoliomonas.

Discoba

Jakobida

OphirininaYabuki, Gyaltshen, Heiss & Kim 2018^[236]
- AgogonidaeGalindo, Prokina, Torruella, López-García & Moreira 2023. Agogonia.^[237]
- OphirinidaeYabuki, Gyaltshen, Heiss & Kim 2018. Ophirina.
AndalucinaCavalier-Smith 2013
- AndaluciidaeCavalier-Smith 2013. Andalucia.
- StygiellidaePánek, Táborský & Čepička 2015.^[238]Stygiella, Velundella.
HistioninaCavalier-Smith 2013. Histiona, Jakoba, Moramonas, Reclinomonas, Seculamonasnomen nudum.

Tsukubamonadida

Tsukubamonas.

Heterolobosea

The phylum Heterolobosea contains around 170 species of amoebae, flagellates, and amoeboflagellates. It was initially established to unite two historically well-known amoeboid orders, Schizopyrenida (such as Naegleria fowleri, a human pathogen) and Acrasida (slime molds). Later, as more flagellates joined this grouping, the usage of Heterolobosea was split between two meanings: the more common usage applies to the entire clade,^[10] while the usage by Cavalier-Smith and collaborators was restricted to a paraphyletic class of "traditional" heteroloboseans, with the name Percolozoa used for the phylum instead.^[241]^[242] The first comprehensive phylogenomic study of Heterolobosea was published in 2025 by Tomáš Pánek and coauthors, resulting in its modern classification.^[239]

Phylum HeteroloboseaPage & Blanton 1985 sensu Hanousková et al. 2019 (=Percolozoa Cavalier-Smith 1991)

Subphylum PharyngomonadaCavalier-Smith 2008
- Class PharyngomonadeaCavalier-Smith in Cavalier-Smith & Nikolaev 2008
  - Order PharyngomonadidaCavalier-Smith in Cavalier-Smith & Nikolaev 2008
    - Family PharyngomonadidaeCavalier-Smith in Cavalier-Smith & Nikolaev 2008, genus Pharyngomonas.
Subphylum TetramitiaCavalier-Smith 1993
- Multisulcus malaysiensisProkina et al. 2025, nom. prov.^[240]
- Family OrodruinidaeShɨshkin 2021^[v] (=Gruberellidae Page & Blanton 1985), genera Orodruina (=Gruberella), Stachyamoeba, Mombasina.^[243]
- Class SelenaioneaPánek & Čepička 2025
  - Order NeovahlkampfiidaCavalier-Smith 2022 emend. Pánek et al. 2025
    - Family NeovahlkampfiidaeHanousková et al. 2018, genus Neovahlkampfia.
  - Order SelenaionidaHanousková et al. 2018
    - Family SelenaionidaeHanousková et al. 2018, genus Selenaion.
- Class EutetramiteaPánek & Čepička 2025. Genera not assigned to any order and family: Eltonia,^[244]Euplaesiobystra, Fumarolamoeba, Heteramoeba, Parafumarolamoeba, Paravahlkampfia, Oramoeba, Vrihiamoeba.
  - Order NaegleriidaPánek & Čepička 2025 (=Heterolobosea sensu Cavalier-Smith 2022). Genera not assigned to any family: Aurem, Marinamoeba.
    - Family AcrasidaePoche 1913, genera Acrasis, Allovahlkampfia, Pocheina.
    - Family NaegleriidaeKudo 1954 emend. Pánek et al. 2025, genera Naegleria, Willaertia, Trimastigamoeba.
    - Family TulamoebidaeKirby et al. 2015, genera Halosymphonia,^[245]Pleurostomum, Tulamoeba.
    - Family VahlkampfiidaeJollos 1917 emend. Pánek et al. 2025, genera Tetramitus, Vahlkampfia, Pseudovahlkampfia, Tetramastigamoeba.
  - Order PercolomonadidaCavalier-Smith 1993
    - Family BarbeliidaeArndt 2023, genera Barbelia, Nonamonas.
    - Family LulaidaeHohlfeld & Arndt 2023, genus Lula.
    - Family PercolomonadidaeCavalier-Smith 2003, genus Percolomonas.
  - Order PseudociliatidaCorliss & Lipscomb 1982
    - Family StephanopogonidaeCorliss 1961, genus Stephanopogon.
  - Order CreneidaCavalier-Smith 2022
    - Family CreneidaePánek et al. 2014, genus Creneis.
  - Order LyromonadidaCavalier-Smith 1993
    - Family PsalteriomonadidaeCavalier-Smith 1993, genera Harpagon, Psalteriomonas (incl. Sawyeria),^[246]Monopylocystis, Pseudoharpagon, Lyromonas.

Euglenozoa

The phylum Euglenozoa is home to at least 2,000 described species of single-celled flagellates of very dissimilar lifestyles. It was originally proposed to group the euglenids (such as the photosynthetic Euglena) and the kinetoplastids (like the pathogenic Trypanosoma), usually studied separatedly; eventually it included diplonemids and symbiontids as well.^[247]^[248]^[249] Due to its share of photosynthetic species, traditionally regarded as algae, the phylum is also known as Euglenophyta by phycologists, and euglenids in particular were often studied as algae. Euglenids and kinetoplastids are the most diverse in terms of described species, although diplonemids may compose over 67,000 potential species.^[249] The classification of euglenozoans was summarized by Cavalier-Smith in 2016.^[248] A more phylogenetically precise revision of their classification was published in 2021 by Alexei Kostygov and coauthors,^[249] with newer clades and genera described in the following years, particularly of euglenids. Still, one group of euglenids, the paraphyletic "ploeotids",^[250] remains unresolved in the current classification, spread out across multiple clades.^[251]^[252]^[253]

Phylum Euglenozoa (Euglenophyta) Cavalier-Smith 1981 emend. Simpson 1997

Class EuglenidaBütschli 1884 emend. Simpson 1997 (=Euglenoida Bütschli 1884 emend. Cavalier-Smith 1993). Genera not assigned to any lower clade: †Moyeria,^[254]Entosiphon. Genera incertae sedis: Gaulosia, Parastasiella, Dinemula, Paradinemula, Mononema, Ovicola, Embryocola, Copromonas.
- Order PetalomonadidaCavalier-Smith 1993
  - Family ScytomonadidaeStein 1878, genera Atraktomonas, Michajlowastasia, Biundula, Calycimonas, Dolium, Dylakosoma, Notosolenus, Pentamonas, Petalomonas^(P), Scytomonas, Tonotosolenus, Tropidoscyphus, Unotosolenus.
  - Family SphenomonadidaeKent 1880, genus Sphenomonas.
- AlistosaLax & Simpson 2021, genera Ploeotia, Serpenomonas, Keelungia, Lentomonas, Decastava.
- KaraviaLax, Cho & Keeling 2023, genera Hemiolia, Liburna.
- OlkaspiraLax & Simpson 2021. Genera not assigned to any lower clade: Chelandium, Olkasia.
  - SpirocutaCavalier-Smith, Chao & Vickerman 2016 (=Helicales Perschke et al. 2017). Genus incertae sedis: Heteronema.
    - AnisonemiaCavalier-Smith 2016
      - Order AnisonemidaCavalier-Smith 2016, family AnisonemidaeKent 1880 emend. Cavalier-Smith 2016, genera Anisonema, Dinema (=Dinematomonas).
      - Order NatomonadidaCavalier-Smith 2016
        Suborder Metanemina, Cavalier-Smith 2016, family NeometanemidaeCavalier-Smith 2016, genus Neometanema.
        AphageaCavalier-Smith 1993 emend. Busse & Preisfeld 2003 (=Rhabdomonadina Leedale 1967 emend. Cavalier-Smith 1993)
        Family AstasiidaeKent 1884, genera Astasia, Gyropaigne, Menoidium, Parmidium, Rhabdomonas.
        Family DistigmidaeHollande 1942, genus Distigma.
    - Order Peranemida (Peranematales) Cavalier-Smith 1993, family Peranemidae (Peranemataceae) Bütschli 1884, genera Chasmostoma, Jenningsia (=Peranemopsis),^[255]Peranema, Teloprocta, Urceolus (=Urceolopsis, Phialonema).^[256]^[257]
    - EuglenophyceaeSchoenichen in Eyfurth & Shoenichen 1925, emend. Marin & Melkonian 2003 (=Euglenea Butschli 1884, emend. Busse & Preisfeld 2002). Genera incertae sedis: Ascoglena, Euglenamorpha, Euglenopsis, Glenoclosterium, Hegneria, Klebsina, Euglenocapsa.
      - Order RapazidaCavalier-Smith 2016, family RapazidaeCavalier-Smith 2016, genus Rapaza.
      - Subclass EuglenophycidaeBusse & Preisfeld, 2003
        Order Eutreptiales (Eutreptiida) Leedale 1967 emend. Marin & Melkonian 2003, family Eutreptiaceae (Eutreptiidae) Hollande 1942, genera Eutreptia, Eutreptiella^(P).
        Order Euglenales (Euglenida) Leedale 1967 emend. Marin & Melkonian 2003
        Family Phacaceae (Phacidae) Kim et al. 2010, genera Discoplastis, Flexiglena, Lepocinclis, Phacus.
        Family Euglenaceae (Euglenidae) Dujardin 1841, emend. Kim et al. 2010, genera Colacium, Cryptoglena, Euglena, Euglenaformis, Euglenaria, Monomorphina, Strombomonas, Trachelomonas.
Class SymbiontidaYubuki, Edgcomb, Bernhard & Leander 2009 (=Postgaardea Cavalier-Smith, 1998), genera Bihospites, Calkinsia, Postgaardi.
Class DiplonemeaCavalier-Smith 1993, order DiplonemidaCavalier-Smith 1993
- Family DiplonemidaeCavalier-Smith 1993 emend. Adl et al. 2019, genera Diplonema, Rhynchopus, Lacrimia, Sulcionema, Flectonema.
- Family HemistasiidaeCavalier-Smith 2016 emend. Adl et al. 2019, genera Hemistasia, Namystinia, Artemidia.
- Family EupelagonemidaeOkamoto & Keeling 2018, genus Eupelagonema.
Class KinetoplasteaHonigberg 1963 emend. Vickerman 1976. Genera incertae sedis: Bordnamonas, Cephalothamnium, Desmomonas, Jarrellia, Lamellasoma.
- Subclass ProkinetoplastinaVickerman in Moreira et al. 2004, order ProkinetoplastidaVickerman in Moreira et al. 2004
  - Family IchthyobodonidaeIsaksen et al. 2007, genus Ichthyobodo.
  - Family PerkinselidaeKostygov in Kostygov et al. 2021, genus Perkinsela (="Perkinsiella",^[258]Hollandeia).^[24]
- Subclass MetakinetoplastinaVickerman in Moreira et al. 2004
  - Order NeobodonidaVickerman in Moreira et al. 2004
    - Suborder NeobodoninaCavalier-Smith 2016
      - Family Neobodonidae^(P?)Cavalier-Smith 2016, genera Actuariola, Avlakibodo,^[259]Azumiobodo, Cruzella, Cryptaulaxella, Klosteria, Neobodo, Phanerobia, Rhynchobodo.
      - Family RhynchomonadidaeCavalier-Smith 2016, genera Dimastigella, Rhynchomonas.
    - Family AllobodonidaeGoodwin, Lee, Kugrens & Simpson 2018,^[260] genera Allobodo, Novijibodo.^[261]
  - Order ParabodonidaVickerman in Moreira et al. 2004
    - Family CryptobiidaePoche 1911 emend. Kostygov in Kostygov et al. 2021, genera Cryptobia, Parabodo.
    - Family TrypanoplasmatidaeHartmann & Chagas 1910 emend. Kostygov in Kostygov et al. 2021, genera Procryptobia, Trypanoplasma.
  - Order EubodonidaVickerman in Moreira et al. 2004, family BodonidaeBütschli 1883, genus Bodo.
  - Order TrypanosomatidaKent 1880 emend. Vickerman in Moreira et al. 2004, family TrypanosomatidaeDolfein 1901. Genera not assigned to subfamilies: Jaenimonas, Vickermania, Sergeia, Wallacemonas. Genera incertae sedis: Cercoplasma, Malacozoomonas, Nematodomonas, Rhynchoidomonas, †PaleoleishmaniaG.Poinar & R.Poinar 2004.^[262]
    - Subfamily TrypanosomatinaeDoflein 1901, genus Trypanosoma.
    - Subfamily LeishmaniinaeMaslov & Lukeš 2012
      - Infrafamily CrithidiataeKostygov & Yurchenko 2017, genera Leptomonas, Crithidia, Lotmaria.
      - Infrafamily LeishmaniataeMaslov & Lukeš 2012, genera Leishmania, Porcisia, Endotrypanum, NovymonasZelonia, Borovskyia.
    - Subfamily HerpetomonadinaeAlexeieff 1911 stat. nov., emend. Kostygov & Yurchenko in Kostygov et al. 2021 (=Phytomonadinae Yurchenko, Kostygov, Votýpka & Lukeš 2015), genera Herpetomonas, Lafontella, Phytomonas.
    - Subfamily StrigomonadinaeVotýpka, Yurchenko, Kostygov & Lukeš 2014, genera Angomonas, Strigomonas, Kentomonas.
    - Subfamily BlastocrithidiinaeVotýpka, Yurchenko & Lukeš 2021, genera Blastocrithidia, Obscuromonas.
    - Subfamily BlechomonadinaeVotýpka & Suková 2013, genus Blechomonas.
    - Subfamily ParatrypanosomatinaeVotýpka & Lukeš 2013, genus Paratrypanosoma.

Minor clades

Ancyromonadida

DivimonasBarkhouse, Eglit, Weston & Simpson 2025^[263]
AncyromonadidaeCavalier-Smith 2008. Ancyromonas, Nutomonas.
PlanomonadidaeCavalier-Smith 1993. Fabomonas, Planomonas.

CRuMs

DiphyllateaCavalier-Smith 2003 → DiphylleidaCavalier-Smith 1993 [Anisomonadea Cavalier-Smith 1993 emend. 2000] → DiphylleidaeCavalier-Smith 1993 [Collodictyonidae Brugerolle et al. 2002; Sulcomonadidae Cavalier-Smith 2013]: CollodictyonCarter 1865, DiphylleiaMassart 1920 [AulacomonasSkuja 1939], SulcomonasBrugerolle 2006.
HilomonadeaCavalier-Smith 2008 emend. 2012 → RigifilidaCavalier-Smith in Yabuki et al. 2012 [Micronucleariida Cavalier-Smith 2008]
- MicronucleariidaeCavalier-Smith 2008: MicronucleariaMikrjukov & Mylnikov 2001.
- RigifilidaeYabuki & Cavalier-Smith in Yabuki et al. 2012: RigifilaYabuki & Cavalier-Smith 2012.
GlissodisceaCavalier-Smith 2013 emend. 2021 → MantamonadidaCavalier-Smith in Glücksman et al. 2011 → MantamonadidaeCavalier-Smith in Glücksman et al. 2011: MantamonasGlücksman & Cavalier-Smith 2011.
GlissandridaYazaki et al. 2025^[264] → GlissandridaeYazaki et al. 2025:^[264]GlissandraPatterson and Simpson 1996^[265]

Telonemia

The phylum Telonemia (telonemids) contains a few species of flagellates found in ocean and fresh waters worldwide. It was originally proposed in 2006 for Telonema, a genus of previously uncertain affinity.^[266] Under the Cavalier-Smith system, telonemids were initially classified as a class of Cryptista,^[73] but later analyses consistently recovered it as a separate group.^[18] Until 2019, only two species had been formally described, each belonging to a separate genus,^[267] but environmental DNA sequencing suggested there were many more species not yet described.^[268] Between 2022 and 2025, eight additional species were described along with three new genera, bringing the total number of species to ten.^[269]^[270]^[271]

Phylum TelonemiaShalchian-Tabrizi 2006, class TelonemeaCavalier-Smith 1993, order TelonemidaCavalier-Smith 1993, family TelonemidaeCavalier-Smith 1993, genera Arpakorses, Lateronema, Hyaloria, Microkorses, Telonema.

Protists of uncertain affiliation

Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol,^[272]Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium,^[w]Copromonas, Cyanomastix, Cyclomonas, Cytamoeba, Dallingeria, Dictyomyxa, Dimastigamoeba, Dinemula, Dinoasteromonas, Diplocalium, Diplomita, Diplophysalis, Diploselmis, Dobellina, Ducelleria, Ectobiella, Elaeorhanis, Embryocola, Endemosarca, Endobiella, Endomonas, Endospora, Enteromyxa, Eperythrocytozoon, Errera, Fromentella, Gweamonas,^[273]Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Lagenidiopsis, Liegeosia, Luffisphaera,^[x]Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Paraluffisphaera, Paramonas, Paraplasma, Parastasia, Parastasiella, Peliainia, Peltomonas, Petasaria, Phagodinium, Phanerobia, Phloxamoeba, Phyllomitus, Phyllomonas, Physcosporidium, Pleuophrys, Pleuromastix, Protenterospora, Protomonas, Pseudoactiniscus, Pseudosporopsis, Rhizomonas, Rhynchodinium, Rigidomastix, Schewiakoffia, Sergentella, Sphaerasuctans, Spongastericus, Spongocyclia, Stephanomonas, Strobilomonas, Tetradimorpha, Thaulirens, Topsentella, Toshiba, Trichonema, Urbanella.^[10]

Incertae sedis within SAR: LabyrinthomyxaDubosq 1921^[274]

Notes

↑The first eukaryotes were "neither plants, animals, nor fungi", hence as defined, the Protista would include the earliest common ancestor of all eukaryotes.
↑In the original 4-kingdom model proposed in 1959, Protista included all unicellular microorganisms such as bacteria.
↑The position of the genera Microcorycia, Parmulina, Penardochlamys and Zonomyxa, which were listed in 2002 under family Microcoryciidae, is not clear. They are placed here by morphological characters but this needs to be supported by molecular data.^[10]
1 2 3 4 5The orders Thecamoebida, Dactylopodida, Acanthopodida, Himatismenida and Pellitida were initially divided into families, but phylogenetic analyses haven't supported the monophyly of each family. For this reason, in recent classifications there is no family rank division within it.^[30]^[10]
↑The genus Pessonella could be a synonym of Vannella.^[10]
↑The 2019 revision by the ISOP ignores the grouping of some variosean genera into higher rank clades (orders and families) proposed in older studies, due to the weakly supported SSU rRNA phylogenetic analyses.^[10]
↑The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.^[51]
↑The 2019 revision by the ISOP inaccurately stated that goniomonads are classified as "Cyathomonadacea Pringsheim 1944".^[10] The name Cyathomonadacea does not exist; Pringsheim only described the family Cyathomonadaceae based on the genus Cyathomonas, and later the order Cyathomonadales and class Cyathomonadea were described, each by different authors. However, as pointed out in 1993 by Gianfranco Novarino and Ian Lucas, this genus was based on a species that actually belonged to Goniomonas; since then, taxonomists have prioritized higher taxa named after it (Goniomonadaceae, Goniomonadales/adida, Goniomonadea) instead.^[74]
↑The genus Tetragonidium is known only from one written diagnosis and some illustrations, and its affinities with cryptomonads are very uncertain.^[74]
↑Within the order Anoecida, the four families Anoecaceae, Caecitellaceae, Cafeteriaceae and Symbiomonadaceae were included by T. Cavalier-Smith in 2006. In a 2013 revision, he simplified the classification by transferring Symbiomonadaceae and Anoecaceae to Cafeteriaceae.^[88] However, both of those families remain accepted by the scientific community as independent from Cafeteriaceae as of 2020.^[93]
↑O'Kelly placed the genera Antarctosaccion, Chrysomeris, Chrysonephos, Nematochrysis/Chrysowaernella, Phaeosaccion and Rhamnochrysis in the order Chrysomeridales nomen nudum in 1989,^[109] and Cavalier-Smith placed it inside the class Chrysomeridophyceae (spelt originally as Chrysomerophycea) in 1995.^[110] However, the class was proven to be polyphyletic. As a result, some of its genera (Nematochrysis/Chrysowaerella) were transferred to the class Chrysoparadoxophyceae, while others (Antarctosaccion and Phaeosaccion) were transferred to the class Phaeosacciophyceae. Due to a lack of molecular data, the placement of Chrysomeris, Chrysonephos and Rhamnochrysis remains unknown.^[111]
↑The position of Eustigmatophyceae is still unstable, with different phylogenetic methodologies showing affinities to either of the SI and SII clades.^[113]^[114]
1 2 3 4 5 6The taxonomic ranks above class level (phylum, subphylum, infraphylum, etc.) are unstable within the Alveolata, due to the many different existing classifications. For example, the phylum-level rank has been traditionally assigned to Perkinsozoa,^[128] Dinoflagellata, Chromerida and Apicomplexa, all of which have been classified as phylum Myzozoa,^[129] which in turn has been classified inside phylum Miozoa.^[117] Treating the four myzozoan groups as separate phyla is generally accepted among phycologists,^[130] while at the same time the rejection of higher taxonomic ranks due to being superfluous is prevalent among protistologists.^[10]
↑Apart from morphological descriptions, no molecular analysis has solidly affiliated Rastrimonas with the Perkinsozoa.^[131]
↑The genera Parallobiopsis, Ellobiocystis and Rhizellobiopsis are only provisionally placed among ellobiopsids.^[142]
↑Highly divergent 18S rRNA.^[10] Since 2020 member of newly identified major apicomplexan subgroup Marosporida, putting together Aggregata octopianaFrenzel 1885, Merocystis kathaeDakin, 1911 (both Aggregatidae, originally coccidians), Rhytidocystis sp. 1 and Rhytidocystis sp. 2 Janouškovec et al. 2019 (RhytidocystidaeLevine, 1979, originally coccidians, Agamococcidiorida), and Margolisiella islandicaKristmundsson et al. 2011 (closely related to Rhytidocystidae)^[147]
↑This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.^[10]
↑There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.^[10]
↑According to Nakamura & Suzuki, the only extant (i.e. not extinct) orders of Polycystinea are Spumellaria, Nassellaria, Collodaria and Orodaria. Therefore, Entactinaria is considered an exclusively fossil group.^[199]
↑One 18S rRNA phylogenetic analysis suggests that the genus Opisthomitus is affiliated with the family Pyrsonymphidae.^[219]
↑Regarding the classification of Retortamonadida, there is a disconnect between the Cavalier-Smith system and the system described by different authors in the Handbook of the protists and other studies. The order Retortamonadida was originally defined as two genera: Chilomastix and Retortamonas. In 2013, Cavalier-Smith modified the retortamonads to only include Retortamonas, and describing a separate order Chilomastigida for Chilomastix only, placed among the early branching Carpediemonas-like organisms.^[228] However, this has not yet been recognized by later studies from the other authors.^[221]^[229]^[230]
↑The family Orodruinidae is possibly polyphyletic, and its type genus Orodruina may belong to the order Neovahlkampfiida.^[239]
↑Probably a synonym of the zygomycete fungus Nephridiophaga.^[10]
↑May be the same genus as Belonocystis.^[10]

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12345Jiang, Chuanhao; Lacante, Siti Arifah; Mizuno, Tetsushi; Syafruddin, Din; Tokoro, Masaharu (2025-03-27). "Genetic diversity of genus Chilomastix: molecular classification of C. mesnili and other potential species variations in humans and animals". Tropical Medicine and Health. 53 (1): 40. doi:10.1186/s41182-025-00725-5. ISSN 1349-4147. PMC 11948686. PMID 40140892.
↑Jiang, Chuanhao; Lacante, Siti Arifah; Mizuno, Tetsushi; Syafruddin, Din; Tokoro, Masaharu (2025-03-27). "Genetic diversity of genus Chilomastix: molecular classification of C. mesnili and other potential species variations in humans and animals". Tropical Medicine and Health. 53 (1): 40. doi:10.1186/s41182-025-00725-5. ISSN 1349-4147. PMC 11948686. PMID 40140892.
↑Vargová, Romana; Hanousková, Pavla; Salamonová, Jana; Žihala, David; Silberman, Jeffrey D.; Eliáš, Marek; Čepička, Ivan (2022-05-19). "Evidence for an Independent Hydrogenosome-to-Mitosome Transition in the CL3 Lineage of Fornicates". Frontiers in Microbiology. 13. doi:10.3389/fmicb.2022.866459. ISSN 1664-302X. PMC 9161772. PMID 35663895.
↑Cavalier-Smith, Thomas (May 2013). "Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa". European Journal of Protistology. 49 (2): 115–178. doi:10.1016/j.ejop.2012.06.001. PMID 23085100.
↑Yubuki, Naoji; Huang, Sam S.C.; Leander, Brian S. (2016). "Comparative Ultrastructure of Fornicate Excavates, Including a Novel Free-living Relative of Diplomonads: Aduncisulcus paluster gen. et sp. nov". Protist. 167 (6): 584–596. doi:10.1016/j.protis.2016.10.001. PMID 27816016.
↑Yubuki, Naoji; Zadrobílková, Eliška; Čepička, Ivan (2017). "Ultrastructure and Molecular Phylogeny of Iotanema spirale gen. nov. et sp. nov., a New Lineage of Endobiotic Fornicata with Strikingly Simplified Ultrastructure". Journal of Eukaryotic Microbiology. 64 (4): 422–433. doi:10.1111/jeu.12376. ISSN 1066-5234. PMID 27749017.
↑Jiang, Chuanhao; Lacante, Siti Arifah; Mizuno, Tetsushi; Syafruddin, Din; Tokoro, Masaharu (2025-03-27). "Genetic diversity of genus Chilomastix: molecular classification of C. mesnili and other potential species variations in humans and animals". Tropical Medicine and Health. 53 (1): 40. doi:10.1186/s41182-025-00725-5. ISSN 1349-4147. PMC 11948686. PMID 40140892.
↑Jiang, Chuanhao; Lacante, Siti Arifah; Mizuno, Tetsushi; Syafruddin, Din; Tokoro, Masaharu (2025-03-27). "Genetic diversity of genus Chilomastix: molecular classification of C. mesnili and other potential species variations in humans and animals". Tropical Medicine and Health. 53 (1): 40. doi:10.1186/s41182-025-00725-5. ISSN 1349-4147. PMC 11948686. PMID 40140892.
1 2 3Poinar, George (2009). "Early Cretaceous protist flagellates (Parabasalia: Hypermastigia: Oxymonada) of cockroaches (Insecta: Blattaria) in Burmese amber". Cretaceous Research. 30 (5): 1066–1072. Bibcode:2009CrRes..30.1066P. doi:10.1016/j.cretres.2009.03.008.
↑Williams, Shelby K.; Jerlström Hultqvist, Jon; Eglit, Yana; Salas-Leiva, Dayana E.; Curtis, Bruce; Orr, Russell J. S.; Stairs, Courtney W.; Atalay, Tuğba N.; MacMillan, Naomi; Simpson, Alastair G. B.; Roger, Andrew J. (2024-08-09). "Extreme mitochondrial reduction in a novel group of free-living metamonads". Nature Communications. 15 (1): 6805. doi:10.1038/s41467-024-50991-w. ISSN 2041-1723. PMC 11316075. PMID 39122691.
↑Shiratori, Takashi; Eglit, Yana; Yazaki, Euki; Inagaki, Yuji; Simpson, Alastair G. B. (2026). "Morphology, Ultrastructure, and Classification of Barthelonids (Metamonada Incertae Sedis): With Descriptions of Microbarthelona Gen. Nov., and Parabarthelona Gen. Nov". Journal of Eukaryotic Microbiology. 73 (3) e70080. doi:10.1111/jeu.70080. PMC 13087550. PMID 41992732.
↑Yabuki A, Gyaltshen Y, Heiss AA, Fujikura K, Kim E (2018). "Ophirina amphinema n. gen., n. sp., a New Deeply Branching Discobid with Phylogenetic Affinity to Jakobids". Scientific Reports. 8 (1) 16219. Bibcode:2018NatSR...816219Y. doi:10.1038/s41598-018-34504-6. PMC 6212452. PMID 30385814.
↑Galindo LJ, Prokina K, Torruella G, López-García P, Moreira D (April 2023). "Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch". Genome Biology and Evolution. 15 (4) evad058. doi:10.1093/gbe/evad058. PMC 10139444. PMID 37029959.
↑Pánek T, Táborský P, Pachiadaki MG, Hroudová M, Vlček Č, Edgcomb VP, Čepička I (2015). "Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage". Frontiers in Microbiology. 6: 1288. doi:10.3389/fmicb.2015.01288. PMC 4649034. PMID 26635756.
1 2 3Pánek, Tomáš; Tice, Alexander K.; Corre, Pia; Hrubá, Pavla; Žihala, David; et al. (16 January 2025). "An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group". Molecular Phylogenetics and Evolution. 204 108289. Bibcode:2025MolPE.20408289P. doi:10.1016/j.ympev.2025.108289. PMID 39826589.
1 2Prokina, Kristina I.; Yubuki, Naoji; Galindo, Luis Javier; Torruella, Guifré; Inagaki, Yuji; Iwamoto, Koji; López-García, Purificación; Moreira, David (September 2025). "A Deeply Branching Lineage in Heterolobosea (Discoba) With Multiflagellated and Multigrooved Life Stages". Journal of Eukaryotic Microbiology. 72 (5) e70037. doi:10.1111/jeu.70037. ISSN 1550-7408. PMC 12328842. PMID 40770464.
↑Cavalier-Smith, Thomas (1993). "Kingdom Protozoa and its 18 phyla". Microbiological Reviews. 57 (4): 953–994. doi:10.1128/mr.57.4.953-994.1993. PMC 372943. PMID 8302218.
↑Pánek, Tomáš; Simpson, Alastair G. B.; Brown, Matthew W.; Dyer, Betsey Dexter (2017). "Heterolobosea". In Archibald, John M.; Simpson, Alastair G.B.; Slamovits, Claudio H. (eds.). Handbook of the Protists. Vol. 2 (2nd ed.). Cham: Springer International Publishing. pp. 1005–1046. doi:10.1007/978-3-319-28149-0_10. ISBN 978-3-319-28149-0. LCCN 2017945328.
↑Tekle, Yonas I.; Wang'ondu, Virginia W.; Ghebezadik, Saron; Cooper, Kennedy S. (31 March 2026). "Quantifying genus-level divergence using 18S rDNA and its application to heterolobosea with discovery of a novel genus from Mombasa Kenya". Scientific Reports. 16 (1) 15233. doi:10.1038/s41598-026-45864-9. ISSN 2045-2322. PMC 13180982. PMID 41917144.
↑Piven, Ekaterina; Kudryavtsev, Alexander (2026). "Eltonia chernetsovi gen. et sp. nov. (Heterolobosea, Eutetramitea) from an ecologically diverse clade comprising closely related soil and seawater species". European Journal of Protistology. 103 126183. doi:10.1016/j.ejop.2026.126183.
↑Lee, Hyeon Been; Park, Jong Soo (2026). "An Amoeboflagellate Halosymphonia sogumizoara gen. et sp. nov . (Tulamoebidae) in Heterolobosea Enhances the Core Halophilic Radiation of Eukaryotes". Journal of Eukaryotic Microbiology. 73 (3) e70083. doi:10.1111/jeu.70083.
↑Foučková, Martina; Uhrová, Kristýna; Kubánková, Aneta; Pánek, Tomáš; Čepička, Ivan (1 April 2024). "Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea)". European Journal of Protistology. 93 126052. doi:10.1016/j.ejop.2024.126052.
↑Simpson, Alastair G.B. (1997). "The identity and composition of the Euglenozoa". Archiv für Protistenkunde. 148 (3): 318–328. doi:10.1016/S0003-9365(97)80012-7.
1 2Cavalier-Smith, Thomas (2016). "Higher classification and phylogeny of Euglenozoa". European Journal of Protistology. 56: 250–276. doi:10.1016/J.EJOP.2016.09.003. PMID 27889663.
1 2 3Kostygov, Alexei Y.; Karnkowska, Anna; Votýpka, Jan; Tashyreva, Daria; Maciszewski, Kacper; et al. (2021). "Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses". Open Biology. 11 (3) 200407. doi:10.1098/rsob.200407. PMC 8061765. PMID 33715388.
↑Lax, Gordon; Lee, Won Je; Eglit, Yana; Simpson, Alastair (2019). "Ploeotids Represent Much of the Phylogenetic Diversity of Euglenids". Protist. 170 (2): 233–257. doi:10.1016/J.PROTIS.2019.03.001. PMID 31102975.
↑Lax, G.; Kolisko, M.; Eglit, Y.; Lee, W.J.; Yubuki, N.; et al. (June 2021). "Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs". Molecular Phylogenetics and Evolution. 159 107088. Bibcode:2021MolPE.15907088L. doi:10.1016/j.ympev.2021.107088. PMID 33545276.
↑Lax, Gordon; Cho, Anna; Keeling, Patrick J. (13 March 2023). "Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree". Journal of Eukaryotic Microbiology. 70 (4) e12973. doi:10.1111/jeu.12973. ISSN 1066-5234. PMID 36912454.
↑Lee, Won Je; Lax, Gordon; Weston, Elizabeth J.; Packer, Julia A.; Hall, Alexandra; Kim, Sun Young; Jeong, Dong Hyuk; Simpson, Alastair G. B. (2026). "A Revised Understanding of Petalomonad Diversity (Petalomonadida; Euglenida) Enabled by a Cultivation Approach, With Five New Species and Two New Genera". Journal of Eukaryotic Microbiology. 73 (3) e70073. doi:10.1111/jeu.70073. ISSN 1066-5234. PMC 13093001. PMID 42003234.
↑Strother, Paul K.; Taylor, Wilson A.; van de Schootbrugge, Bas; Leander, Brian S.; Wellman, Charles H. (2020). "Pellicle ultrastructure demonstrates that Moyeria is a fossil euglenid". Palynology. 44 (3): 461–471. Bibcode:2020Paly...44..461S. doi:10.1080/01916122.2019.1625457.
↑Lee WJ, Blackmore R, Patterson DJ (1999). "Australian records of two lesser known genera of heterotrophic euglenids – Chasmostoma Massart, 1920 and Jenningsia Schaeffer, 1918". Protistology. 1: 10–16.
↑Larsen, Jacob; Patterson, David J. (1990). "Some flagellates (Protista) from tropical marine sediments". Journal of Natural History. 24 (4): 801–937. Bibcode:1990JNatH..24..801L. doi:10.1080/00222939000770571.
↑Lax, Gordon; Simpson, Alastair G.B. (2020). "The Molecular Diversity of Phagotrophic Euglenids Examined Using Single-cell Methods". Protist. 171 (5) 125757. doi:10.1016/J.PROTIS.2020.125757. PMID 33126020.
↑Dyková, Iva; Fiala, Ivan; Pecková, Hana (2008). "Neoparamoeba spp. and their eukaryotic endosymbionts similar to Perkinsela amoebae (Hollande, 1980): Coevolution demonstrated by SSU rRNA gene phylogenies". European Journal of Protistology. 44 (4): 269–277. doi:10.1016/j.ejop.2008.01.004. PMID 18396388.
↑Belyaev, Artem O.; Zagumyonnyi, Dmitriy G.; Mylnikov, Alexander P.; Tikhonenkov, Denis V. (2022). "The Morphology, Ultrastructure and Molecular Phylogeny of a New Soil-Dwelling Kinetoplastid Avlakibodo gracilis gen. et sp. nov. (Neobodonida; Kinetoplastea)". Protist. 173 (4) 125885. doi:10.1016/j.protis.2022.125885. PMID 35667307. S2CID 248711669.
↑Goodwin, Joshua D.; Lee, Thomas F.; Kugrens, Paul; Simpson, Alastair G.B. (1 August 2018). "Allobodo chlorophagus n. gen. n. sp., a Kinetoplastid that Infiltrates and Feeds on the Invasive Alga Codium fragile". Protist. 169 (6): 911–925. doi:10.1016/j.protis.2018.07.001. PMID 30445354.
↑Packer, Julia A.; Zavadska, Daryna; Weston, Elizabeth J.; Eglit, Yana; Richter, Daniel J.; Simpson, Alastair G.B. (27 January 2025). "Characterization of Allobodo yubaba sp. nov. and Novijibodo darinka gen. et sp. nov., cultivable free-living species of the phylogenetically enigmatic kinetoplastid taxon Allobodonidae". Journal of Eukaryotic Microbiology. 72 (1) e13072. doi:10.1111/jeu.13072. PMC 11771631. PMID 39868642.
↑Poinar, George; Poinar, Roberta (1 September 2004). "Paleoleishmania proterus n. gen., n. sp., (Trypanosomatidae: Kinetoplastida) from Cretaceous Burmese Amber". Protist. 155 (3): 305–310. doi:10.1078/1434461041844259. PMID 15552057.
↑Barkhouse, Kate M.; Eglit, Yana; Weston, Elizabeth J.; Jenkins, Adriana B. A.; Simpson, Alastair G. B. (2025). "Cultivation of Ancyromonas melba, and Reclassification as the Type Species of Divimonas gen. nov., a Phylogenetically Important Ancyromonad Lineage". Journal of Eukaryotic Microbiology. 72 (2) e70005. doi:10.1111/jeu.70005. PMC 11891473. PMID 40059502.
1 2Yazaki, Euki; Harada, Ryo; Isogai, Ryu; Bamba, Kohei; Ishida, Ken-ichiro; Inagaki, Yuji; Shiratori, Takashi (June 2025). "Glissandra oviformis n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs". Open Biology. 15 (6) 250057. doi:10.1098/rsob.250057. PMC 12133344. PMID 40460873.
↑Patterson, David J.; Simpson, A.G.B. (December 1996). "Heterotrophic flagellates from coastal marine and hypersaline sediments in Western Australia". European Journal of Protistology. 32 (4): 423–448. doi:10.1016/S0932-4739(96)80003-4.
↑Shalchian-Tabrizi, K; Eikrem, W; Klaveness, D; Vaulot, D; Minge, M.A; Le Gall, F; Romari, K; Throndsen, J; Botnen, A; Massana, R; Thomsen, H.A; Jakobsen, K.S (28 April 2006). "Telonemia, a new protist phylum with affinity to chromist lineages". Proceedings of the Royal Society B: Biological Sciences. 273 (1595): 1833–1842. doi:10.1098/rspb.2006.3515. PMC 1634789. PMID 16790418.
↑Strassert, Jürgen F H; Jamy, Mahwash; Mylnikov, Alexander P; Tikhonenkov, Denis V; Burki, Fabien; Shapiro, Beth (April 2019). "New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life". Molecular Biology and Evolution. 36 (4): 757–765. doi:10.1093/molbev/msz012. PMC 6844682. PMID 30668767.
↑Shalchian-Tabrizi, K; Kauserud, H; Massana, R; Klaveness, D; Jakobsen, KS (18 April 2007). "Analysis of Environmental 18S Ribosomal RNA Sequences reveals Unknown Diversity of the Cosmopolitan Phylum Telonemia". Protist. 158 (2): 173–180. doi:10.1016/j.protis.2006.10.003. PMID 17196879.
↑Tikhonenkov DV, Jamy M, Borodina AS, Belyaev AO, Zagumyonnyi DG, Prokina KI, Mylnikov AP, Burki F, Karpov SA (2022). "On the origin of TSAR: morphology, diversity and phylogeny of Telonemia". Open Biology. 12 (3) 210325. doi:10.1098/rsob.210325. PMC 8924772. PMID 35291881.
↑Zlatogursky, Vasily; Boscaro, Vittorio; Lax, Gordon; Wanntorp, Matias; Pohl, Nina; Burki, Fabien; Keeling, Patrick J. (15 August 2025). "Phylogenetic position and mitochondrial genome evolution of "orphan" eukaryotic lineages". iScience. 28 (8) 113184. doi:10.1016/j.isci.2025.113184. PMC 12432456. PMID 40948565.
↑Mostazo‐Zapata, Helena; Gàlvez‐Morante, Alex; Berney, Cédric; Maya‐Figuerola, Xènia; Sigona, Cristiana; López‐Escardó, David; Sà, Elisabet L.; Vaqué, Dolors; Richter, Daniel J. (2025). "Description of a New Telonemia Genus and Species With Novel Observations Providing Insights Into Its Hidden Diversity". Journal of Eukaryotic Microbiology. 72 (6) e70050. doi:10.1111/jeu.70050. ISSN 1066-5234. PMC 12550356. PMID 41131848.
↑Shishkin, Yegor; Drachko, Daria; Zlatogursky, Vasily V. (22 April 2021). "The smallest known heliozoans are the Erebor lineage (nom. clad. n.) inside Microheliella maris (Eukaryota, Diaphoretickes), with the amendation of M. maris diagnosis and description of Berkeleyaesol magnus gen. nov., comb. nov. (Eukaryota, incertae sedis)". International Journal of Systematic and Evolutionary Microbiology. 71 (4). doi:10.1099/ijsem.0.004776. PMID 33886450. S2CID 233370018.
↑Lee, Won Je (2002). "Some free-living heterotrophic flagellates from marine sediments of inchon and Ganghwa Island, Korea". Korean Journal of Biological Sciences. 6 (2): 125–143. doi:10.1080/12265071.2001.9647643.
↑Anderson, O. Roger; Cavalier-Smith, Thomas (2012). "Ultrastructure of Diplophrys parva, a New Small Freshwater Species, and a Revised Analysis of Labyrinthulea (Heterokonta)". Acta Protozoologica. 51: 291–304. doi:10.4467/16890027AP.12.023.0783.

External links

EukMap – Taxonomy Map of the UniEuk Project

[origin-1] The first eukaryotes were "neither plants, animals, nor fungi", hence as defined, the Protista would include the earliest common ancestor of all eukaryotes.

[3] In the original 4-kingdom model proposed in 1959, Protista included all unicellular microorganisms such as bacteria.

[33] The position of the genera Microcorycia, Parmulina, Penardochlamys and Zonomyxa, which were listed in 2002 under family Microcoryciidae, is not clear. They are placed here by morphological characters but this needs to be supported by molecular data.^[10]

[nofam-43] 1 2 3 4 5The orders Thecamoebida, Dactylopodida, Acanthopodida, Himatismenida and Pellitida were initially divided into families, but phylogenetic analyses haven't supported the monophyly of each family. For this reason, in recent classifications there is no family rank division within it.^[30]^[10]

[Pessonella-46] The genus Pessonella could be a synonym of Vannella.^[10]

[Variosea-50] The 2019 revision by the ISOP ignores the grouping of some variosean genera into higher rank clades (orders and families) proposed in older studies, due to the weakly supported SSU rRNA phylogenetic analyses.^[10]

[Picozoa-58] The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.^[51]

[82] The 2019 revision by the ISOP inaccurately stated that goniomonads are classified as "Cyathomonadacea Pringsheim 1944".^[10] The name Cyathomonadacea does not exist; Pringsheim only described the family Cyathomonadaceae based on the genus Cyathomonas, and later the order Cyathomonadales and class Cyathomonadea were described, each by different authors. However, as pointed out in 1993 by Gianfranco Novarino and Ian Lucas, this genus was based on a species that actually belonged to Goniomonas; since then, taxonomists have prioritized higher taxa named after it (Goniomonadaceae, Goniomonadales/adida, Goniomonadea) instead.^[74]

[88] The genus Tetragonidium is known only from one written diagnosis and some illustrations, and its affinities with cryptomonads are very uncertain.^[74]

[105] Within the order Anoecida, the four families Anoecaceae, Caecitellaceae, Cafeteriaceae and Symbiomonadaceae were included by T. Cavalier-Smith in 2006. In a 2013 revision, he simplified the classification by transferring Symbiomonadaceae and Anoecaceae to Cafeteriaceae.^[88] However, both of those families remain accepted by the scientific community as independent from Cafeteriaceae as of 2020.^[93]

[Chrysomeridophyceae-122] O'Kelly placed the genera Antarctosaccion, Chrysomeris, Chrysonephos, Nematochrysis/Chrysowaernella, Phaeosaccion and Rhamnochrysis in the order Chrysomeridales nomen nudum in 1989,^[109] and Cavalier-Smith placed it inside the class Chrysomeridophyceae (spelt originally as Chrysomerophycea) in 1995.^[110] However, the class was proven to be polyphyletic. As a result, some of its genera (Nematochrysis/Chrysowaerella) were transferred to the class Chrysoparadoxophyceae, while others (Antarctosaccion and Phaeosaccion) were transferred to the class Phaeosacciophyceae. Due to a lack of molecular data, the placement of Chrysomeris, Chrysonephos and Rhamnochrysis remains unknown.^[111]

[126] The position of Eustigmatophyceae is still unstable, with different phylogenetic methodologies showing affinities to either of the SI and SII clades.^[113]^[114]

[Alveolata-137] 1 2 3 4 5 6The taxonomic ranks above class level (phylum, subphylum, infraphylum, etc.) are unstable within the Alveolata, due to the many different existing classifications. For example, the phylum-level rank has been traditionally assigned to Perkinsozoa,^[128] Dinoflagellata, Chromerida and Apicomplexa, all of which have been classified as phylum Myzozoa,^[129] which in turn has been classified inside phylum Miozoa.^[117] Treating the four myzozoan groups as separate phyla is generally accepted among phycologists,^[130] while at the same time the rejection of higher taxonomic ranks due to being superfluous is prevalent among protistologists.^[10]

[145] Apart from morphological descriptions, no molecular analysis has solidly affiliated Rastrimonas with the Perkinsozoa.^[131]

[157] The genera Parallobiopsis, Ellobiocystis and Rhizellobiopsis are only provisionally placed among ellobiopsids.^[142]

[163] Highly divergent 18S rRNA.^[10] Since 2020 member of newly identified major apicomplexan subgroup Marosporida, putting together Aggregata octopianaFrenzel 1885, Merocystis kathaeDakin, 1911 (both Aggregatidae, originally coccidians), Rhytidocystis sp. 1 and Rhytidocystis sp. 2 Janouškovec et al. 2019 (RhytidocystidaeLevine, 1979, originally coccidians, Agamococcidiorida), and Margolisiella islandicaKristmundsson et al. 2011 (closely related to Rhytidocystidae)^[147]

[Stichotrichida-167] This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.^[10]

[Tracheleuglypha-180] There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.^[10]

[Entactinaria-218] According to Nakamura & Suzuki, the only extant (i.e. not extinct) orders of Polycystinea are Spumellaria, Nassellaria, Collodaria and Orodaria. Therefore, Entactinaria is considered an exclusively fossil group.^[199]

[243] One 18S rRNA phylogenetic analysis suggests that the genus Opisthomitus is affiliated with the family Pyrsonymphidae.^[219]

[251] Regarding the classification of Retortamonadida, there is a disconnect between the Cavalier-Smith system and the system described by different authors in the Handbook of the protists and other studies. The order Retortamonadida was originally defined as two genera: Chilomastix and Retortamonas. In 2013, Cavalier-Smith modified the retortamonads to only include Retortamonas, and describing a separate order Chilomastigida for Chilomastix only, placed among the early branching Carpediemonas-like organisms.^[228] However, this has not yet been recognized by later studies from the other authors.^[221]^[229]^[230]

[264] The family Orodruinidae is possibly polyphyletic, and its type genus Orodruina may belong to the order Neovahlkampfiida.^[239]

[Coelosporidium-295] Probably a synonym of the zygomycete fungus Nephridiophaga.^[10]

[Luffisphaera-297] May be the same genus as Belonocystis.^[10]

[whitaker5kingdoms-2] 1 2Whittaker, R. H. (1969). "New Concepts of Kingdoms of Organisms". Science. 163 (3863): 150–160. Bibcode:1969Sci...163..150W. doi:10.1126/SCIENCE.163.3863.150. PMID 5762760.

[Higher-4] Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M. (2015). "A Higher Level Classification of All Living Organisms". PLOS ONE. 10 (4) e0119248. Bibcode:2015PLoSO..1019248R. doi:10.1371/JOURNAL.PONE.0119248. PMC 4418965. PMID 25923521. (Erratum: doi:10.1371/journal.pone.0130114)

[Torruella-2025-5] Torruella, Guifré; Galindo, Luis Javier; Moreira, David; López-García, Purificación (2025). "Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life". Current Biology. 35 (1): 198–207.e4. Bibcode:2025CBio...35..198T. doi:10.1016/j.cub.2024.10.075. PMID 39642877.

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