Between brackets is the number of accepted species
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- Biota
- Kingdom Animalia
- Kingdom Archaea
- Kingdom Bacteria
- Kingdom Chromista
- Subkingdom Hacrobia
- Subkingdom Harosa
- Infrakingdom Halvaria
- Superphylum Alveolata
- Phylum Acavomonidia
- Phylum Ciliophora
- Phylum Dinophyta accepted as Miozoa
- Phylum Miozoa
- Subphylum Myzozoa
- Infraphylum Apicomplexa
- Infraphylum Dinozoa
- Superclass Dinoflagellata
- Class Dinophyceae
- Order Amphidiniales
- Order Amphilothales
- Order Blastodiniales
- Order Brachidiniales
- Order Chytriodiniales
- Order Desmocapsales
- Order Desmomastigales
- Order Dinamoebales accepted as Dinamoebidiales
- Order Dinamoebidiales
- Order Dinocloniales accepted as Phytodiniales
- Order Dinophyceae incertae sedis
- Order Dinophysales
- Order Gloeodiniales
- Order Gonyaulacales
- Order Gymnodiniales
- Order Haplozoonales
- Order Nannoceratopsiales †
- Order Peridiniales
- Family Archaeosphaerodiniopsidaceae Deflandre in Chatton, 1952, nom. transl.
- Family Biecheleriaceae accepted as Suessiaceae Montresor, Procaccini & Stoecker, 1999
- Family Ceratocorythaceae Lindemann, 1928 accepted as Protoceratiaceae Lindemann, 1928
- Family Congruentidiaceae Schiller, 1935 accepted as Protoperidiniaceae J.P. Bujak & E.H. Davies
- Family Crypthecodiniaceae Biecheler ex Chatton, 1952
- Family Deflandreaceae Eisenack, 1954 † accepted as Peridiniaceae Ehrenberg, 1831
- Family Dinosphaeraceae Lindemann, 1928
- Family Dinotrichaceae accepted as Kryptoperidiniaceae Lindemann, 1926
- Family Diplopsaliaceae Matsuoka, 1988 accepted as Protoperidiniaceae J.P. Bujak & E.H. Davies
- Family Ensiculiferaceae Z. Li, M. Gottschling, K.N. Mertens, H.F. Gu & H.H. Shin in Li et al., 2020
- Family Glenodiniaceae Willey & Hickson, 1909 accepted as Peridiniales incertae sedis
- Family Glenodiniopsidaceae Schiller, 1935
- Family Heterocapsaceae R.A. Fensome, F.J.R. Taylor, G. Norris, W.A.S. Sarjeant, D.I. Wharton & G.L. Williams
- Family Kryptoperidiniaceae Lindemann, 1926
- Family Lessardiaceae Carbonell-Moore, 2004
- Family Oxytoxaceae Lindemann, 1928
- Family Oxytoxidae accepted as Oxytoxaceae Lindemann, 1928
- Family Palaeoperidiniaceae † accepted as Peridiniaceae Ehrenberg, 1831
- Family Peridiniaceae Ehrenberg, 1831
- Family Peridiniales (awaiting allocation)
- Family Peridiniales incertae sedis
- Family Peridiniida incertae sedis
- Family Peridiniidae accepted as Peridiniaceae Ehrenberg, 1831
- Family Peridiniineae (awaiting allocation)
- Family Peridiniopsidaceae M. Gottschling, J. Kretschmann & A. Žerdoner Časalan, 2017
- Family Podolampaceae accepted as Podolampadaceae Lindemann, 1928
- Family Podolampadaceae Lindemann, 1928
- Family Protoperidiniaceae J.P. Bujak & E.H. Davies
- Genus Apsteinia T.H. Abé, 1981 accepted as Diplopsalis Bergh, 1881
- Genus Barssidinium J.K. Lentin, R.A. Fensome & G.L. Williams, 1994 †
- Genus Boreadinium Dodge & Hermes, 1981
- Genus Cangxianella J. Xu, Z. Pan, Y. Yang, Y. Zhu & N. Fan, 1997 †
- Genus Capillicysta K. Matsuoka & J.P. Bujak in K. Matsuoka, J.P. Bujak & T. Shimazaki, 1987 †
- Genus Congruentidium T.H. Abé, 1927 accepted as Protoperidinium Bergh, 1882
- Genus Cristadinium M.J. Head, G. Norris & P.J. Mudie, 1989 †
- Genus Cryodinium O. Esper & K.A.F. Zonneveld, 2002
- Genus Deflagymnium Olaru, 1978 †
- Genus Diplopelta Stein ex Jörgensen, 1912
- Genus Diplopeltopsis Pavillard, 1913 accepted as Preperidinium Mangin, 1913
- Genus Diplopsalis Bergh, 1881
- Genus Diplopsalopsis Meunier, 1910
- Genus Dissodium T.H. Abé, 1941
- Genus Dubridinium P.C. Reid, 1977
- Genus Entzia Lebour, 1922 accepted as Diplopsalis Bergh, 1881
- Genus Erymnodinium J.K. Lentin, R.A. Fensome & G.L. Williams, 1994 †
- Genus Gerlachidium P.N. von Benedek & W.A.S. Sarjeant, 1982 †
- Genus Gotoius T.H. Abé ex Matsuoka, 1988
- Genus Huia H.F. Gu, K.N. Mertens & T.T. Liu, 2016
- Genus Islandinium M.J. Head, R. Harland & J. Matthiessen, 2001
- Genus Lebouraia T.H. Abé ex A. Sournia, 1986
- Genus Leipokatium M.R. Bradford, 1975
- Genus Lejeunecysta D.G. Artzner & G. Dörhöfer, 1978
- Species Lejeunecysta fallax (Morgenroth, 1966) Artzner & Dörhöfer †
- Species Lejeunecysta hyalina (Gerlach, 1961) Lentin & Williams, 1993 †
- Species Lejeunecysta sabrina (P.C. Reid) J.P. Bujak
- Genus Lejeunia Gerlach, 1961 accepted as Lejeunecysta D.G. Artzner & G. Dörhöfer, 1978
- Genus Malvinia A.J. Houben, P.K. Bijl, G.R. Guerstein, A. Sluijs & H. Brinkhuis, 2011 † accepted as Malviniella E.A. Molinari-Novoa & M.D. Guiry, 2021 †
- Genus Malviniella E.A. Molinari-Novoa & M.D. Guiry, 2021 †
- Genus Margosphaera E. Nagy, 1965 † accepted as Selenopemphix P.N. von Benedek, 1972
- Genus Matvienkodinium A.F. Krakhmalny, 2013
- Genus Matvienkoella Ø. Moestrup & A.J. Calado, 2018 accepted as Matvienkodinium A.F. Krakhmalny, 2013
- Genus Miniscula accepted as Minuscula Lebour, 1925
- Genus Minuscula Lebour, 1925
- Genus Multispinula M.R. Bradford, 1975 accepted as Selenopemphix P.N. von Benedek, 1972
- Genus Multispinulosa R. Harland, 1977 † accepted as Multispinula M.R. Bradford, 1975
- Genus Niea T. Liu, K.N. Mertens & H. Gu, 2015
- Genus Nucicla J.D. Hartman, F. Sangiorgi, P.K. Bijl & G.J. Versteegh, 2019 †
- Genus Oblea E. Balech ex A.R. Loeblich Jr. & A.R. Loeblich III, 1966
- Genus Omanodinium M.R. Bradford, 1975 † accepted as Selenopemphix P.N. von Benedek, 1972
- Genus Phelodinium L.E. Stover & W.R. Evitt, 1978 †
- Genus Preperidinium Mangin, 1913
- Genus Properidinium Meunier, 1919 accepted as Archaeperidinium Jörgensen, 1912
- Genus Properidinium Lauterborn, 1894 accepted as Protoperidinium Bergh, 1882
- Genus Protoperidinium Bergh, 1882
- Genus Protoperidium Pouchet, 1882 accepted as Protoperidinium Bergh, 1882
- Genus Pseudoalterbia S.-Z. Mao & G. Norris, 1988 †
- Genus Qia T. Liu, K.N. Mertens & H. Gu, 2015
- Genus Scaldecysta De Schepper, Head & Louwye, 2004 †
- Genus Selenopemphix P.N. von Benedek, 1972
- Genus Stelladinium M.R. Bradford, 1975
- Genus Testeria Faust, 2003 accepted as Protoperidinium Bergh, 1882
- Genus Zygabikodinium Loeblich Jr. & Loeblich III, 1970 accepted as Preperidinium Mangin, 1913
- Family Pyrophacaceae Lindemann, 1928 accepted as Pyrocystaceae (Schütt, 1896) Lemmermann, 1899
- Family Thecadiniaceae
- Order Peridiniphycidae incertae sedis †
- Order Phytodiniales
- Order Prorocentrales
- Order Ptychodiscales accepted as Dinophyceae incertae sedis
- Order Pyrocystales accepted as Gonyaulacales
- Order Suessiales
- Order Thoracosphaerales
- Order Torodiniales
- Order Tovelliales
- Order Zooxanthellales accepted as Suessiales
- Family Apodiniaceae
- Family Apodinidae accepted as Apodiniaceae
- Family Gomesiamonadaceae
- Genus Abantosphaeridium Banerjee & Rawat, 1991 †
- Genus Agrosphaera Haeckel ex Lo Bianco, 1903
- Genus Aidelocysta J.B. Riding, R. Helby & J. Stevens in J.B. Riding & R. Helby, 2001 †
- Genus Ailadinium M. Saburoa & N. Chomérat, 2014
- Genus Ampulladinium J.B. Riding, R. Helby & F.M. Parker in Riding & Helby, 2001 †
- Genus Binzhoudinium J. Xu, Z. Pan, Y. Yang, Y. Zhu & N. Fan, 1997 †
- Genus Bispinodinium N. Yamada & T. Horiguchi in Yamada, Terada, Tanaka & Horiguchi, 2013
- Genus Bonbonadinium R. Helby & A.D. Partridge, 2001 †
- Genus Caspidinium Marret in Marret, Leroy, Chalie & Gasse, 2004 †
- Genus Cavatodissiliodinium Feist-Burkhardt & Monteil, 2001 †
- Genus Chlorodinium R. Chodat, 1921 accepted as Geodinium R. Chodat, 1928
- Genus Costacysta C. Heilmann-Clausen & S. Van Simaeys, 2005 †
- Genus Cygnusicysta J.B. Riding & R. Helby, 2001 †
- Genus Cystodinium Schulz & Mai, 1966 †
- Genus Dinoasteromonas Bursa, 1971
- Genus Discoasteromonas Bursa, 1965
- Genus Dodekovaea E.A. Molinari-Novoa & M.D. Guiry, 2021 †
- Genus Echinocysta J. Xu, Z. Pan, Y. Yang, Y. Zhu & N. Fan, 1997 †
- Genus Echinum A. Meunier, 1910
- Genus Fallaciodinium Harding, 1998 †
- Genus Fosteria J.B. Riding & R. Helby, 2001 † accepted as Fostericysta J.B. Riding, 2006 †
- Genus Fostericysta J.B. Riding, 2006 †
- Genus Geodinium R. Chodat, 1928
- Genus Gleba Bruguière, 1791
- Genus Glenoaulax Diesing, 1866
- Genus Glyphodinium Fresenius, 1865
- Genus Goodwynia D.J. Mantle, J.B. Riding & C. Hannaford, 2020 †
- Genus Guttula Dodekova, 1983 † accepted as Dodekovaea E.A. Molinari-Novoa & M.D. Guiry, 2021 †
- Genus Hadriana J.B. Riding & R. Helby, 2001 †
- Genus Keltoidites Krutzsch & Pacltová, 1991 †
- Genus Kilwacysta E. Schrank, 2005 †
- Genus Lopsidinium G. Dolby, 2014 †
- Genus Madanidinium N. Chomérat in Chomérat & Bilien, 2014
- Genus Moestrupia G. Hansen & N. Daugbjerg, 2011
- Genus Mombasadinium J.B. Riding & R. Helby, 2001 †
- Genus Nenjiangella Yuan & He, 1999 †
- Genus Physalocysta J. Xu, Z. Pan, Y. Yang, Y. Zhu & N. Fan, 1997 †
- Genus Plagiaulax Richard, 1902
- Genus Proaulax Diesing, 1866
- Genus Prolixosphaeridium R.J. Davey, C. Downie, W.A.S. Sarjeant & G.L. Williams, 1966 †
- Genus Pseudadenoides F. Gómez, R. Onuma, L.F. Artigas & T. Horiguchi, 2015
- Genus Pyramidodinium T. Horiguchi & C. Sukigara, 2005
- Genus Radiozoum Mingazzini, 1904
- Genus Shandongidium J. Xu, Z. Pan, Y. Yang, Y. Zhu & N. Fan, 1997 †
- Genus Skuadinium J.B. Riding & R. Helby, 2001 †
- Genus Sphaerosperma Pouchet, 1893
- Genus Spinatipolus Dodekova, 1983 †
- Genus Striatodinium J.B. Riding & R. Helby, 2001 †
- Genus Suibindia J.-X. Yu, 1982 †
- Genus Tringadinium J.B. Riding & R. Helby, 2001 †
- Genus Uralodinium N.K. Lebedeva, 2006 †
- Genus Voodooia J.B. Riding & R. Helby, 2001 †
- Genus Wittnaudinium R. Bucefalo Palliani & J.B. Riding, 1998 †
- Genus Woodinia J.B. Riding & R. Helby, 2001 †
- Genus Xylochoarion U. Erkmen & W.A.S. Sarjeant, 1978 †
- Genus Zoorhabdella L. Rhumbler, 1909
- Class Ellobiopsea
- Class Myzodinea
- Class Noctilucea accepted as Noctiluciphyceae
- Class Noctiluciphyceae
- Class Oxyrrhea
- Class Oxyrrhidophyceae accepted as Oxyrrhea
- Class Syndinea accepted as Syndiniophyceae
- Class Syndiniophyceae
- Genus Eleftheros D.V. Tikhonenkov, E. Hehenberger & P.J. Keeling in Holt et al., 2023
- Superclass Perkinsozoa
- Subphylum Protalveolata
- Order Chilovorida accepted as Colpodellida
- Order Chromerida accepted as Colpodellida
- Order Colpodellida
- Order Voromonadida accepted as Colpodellida
- Superphylum Heterokonta
- Infrakingdom Rhizaria
- Kingdom Fungi
- Kingdom Plantae
- Kingdom Protista accepted as Protozoa
- Kingdom Protozoa
- Kingdom Viruses
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