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
- Superphylum Heterokonta
- Phylum Bacillariophyta
- Class Bacillariophyceae
- Order Achnanthales accepted as Mastogloiales
- Order Ardissoneales accepted as Toxariales
- Order Ardissoniales accepted as Toxariales
- Order Bacillariales
- Order Centrales accepted as Coscinodiscophyceae
- Order Climacospheniales accepted as Toxariales
- Order Cocconeidales
- Order Cyclophorales
- Order Cymbellales
- Order Dictyoneidales
- Order Eunotiales
- Order Fragilariales
- Order Licmophorales
- Order Lyrellales
- Order Mastogloiales
- Order Naviculales
- Order Pennales accepted as Bacillariophyceae
- Order Protoraphidales
- Order Rhabdonematales
- Order Rhaphoneidales
- Order Rhopalodiales
- Order Striatellales
- Order Surirellales
- Order Tabellariales
- Order Thalassionematales
- Order Thalassiophysales
- Family Bacillariophyceae incertae sedis
- Genus Actinoneis Cleve, 1895
- Genus Actinostephanos G.K. Khursevich, 1989
- Genus Aggericorona S. Komura, 2006 †
- Species Aggericorona ponderosa S. Komura, 2006 †
- Genus Ambo A. Witkowski, M. Ashworth, H. Lange-Bertalot & G. Klein in Witkowski et al., 2020
- Genus Amphicephalosperma Meunier
- Genus Amphidiscus Ehrenberg, 1839 †
- Genus Amphidiscus Ehrenberg, 1839, nom. nud. † accepted as Amphidiscus Ehrenberg, 1839 †
- Genus Anisoraphe R.E. Norris, 1971
- Genus Annularius S. Komura, 2005 † accepted as Circularius E.A. Molinari-Novoa, C.E. Sánchez Ocharan & M.D. Guiry in Molinari-Novoa et al., 2021 †
- Genus Aporidiscus Rattray, 1889
- Genus Aporodiscus J. Rattray, 1890
- Genus Apteroe Cleve, 1891
- Genus Archaegoniothecium J. Witkowski, D.M. Harwood & M. Kulikovskiy, 2011 †
- Genus Archeopantocsekia Borbas, 1893 †
- Genus Archimedea Bory de Saint-Vincent, 1824
- Genus Astrosyne M.P. Ashworth & C.S. Lobban in Ashworth, Ruck, Lobban, Romanovicz & Theriot, 2012
- Genus Baculites J. Gruss, 1928
- Genus Bifibulatia H. Takano, 1983
- Genus Bruniella H. Van Heurck, 1896
- Genus Callimastogloia S. Komura, 2005 †
- Genus Calophyllum G. Shadbolt, 1854
- Genus Circularius E.A. Molinari-Novoa, C.E. Sánchez Ocharan & M.D. Guiry in Molinari-Novoa et al., 2021 †
- Genus Cladomphalus J.W. Bailey, 1894
- Genus Clevamphora C. Mereschkowsky, 1903
- Genus Cohaesum V.A. Nikolaev & D.M. Harwood, 2007 †
- Genus Confervea O.F. Muller, 1783
- Genus Creania M. Olney in Olney, Bohaty, Harwood & Scherer, 2009 †
- Genus Cristodiscus Z.I. Glezer & A.P. Olshtynskaya, 1994 †
- Genus Crystalia Sommerfeld, 1824
- Genus Cycloites J. Gruss, 1928
- Genus Cycloplea V.B.A. Trevisan di San Leon, 1848
- Genus Cyclostephanopsis L. Loginova, 1993 †
- Genus Cymatogonia Grunow, 1883
- Genus Cymbamphora Cleve, 1895
- Genus Dalailama Mereschkowsky
- Genus Dalai-Lama C. Mereschkowsky, 1906
- Genus Dandrelion P. Lefebure, 1947
- Genus Dendrelion Pantocsek, 1928
- Genus Diatomosira V.B.A. Trevisan di San Leon, 1848
- Genus Diatostephana E.A. Molinari-Novoa & M.D. Guiry, 2021
- Genus Didymohelix J.W. Griffith
- Genus Dimerosira H. Peragallo, 1901
- Genus Distichanthes Ehrenberg, 1854
- Genus Drepanotheca H.-J. Schrader ex Round, Crawford & Mann, 1990 †
- Genus Dunia V.A. Nikolaev & D.M. Harwood in Nikolaev, Harwood & Samsonov, 2000 †
- Genus Echinaria Kützing, 1844
- Genus Endostauron Brébisson ex Müller, 1892
- Genus Euceratoneis Grunow, 1865
- Genus Excentron J. Ralfs, 1861
- Genus Fibula Wm. Smith, 1859
- Genus Grymaia J.W. Bailey ex L.W. Bailey, 1861
- Genus Halonetrum H. Lohmann
- Genus Halopetitia S. Blanco & C.E. Wetzel, 2016
- Genus Harrisonii E.M. Nelson
- Genus Haynaldiella Pantocsek ex H. Van Heurck, 1896
- Genus Heliodiscus H. van Heurck ex G. Karsten, 1928
- Genus Helissella Jurilj
- Genus Hendeyscoresbya S. Blanco & C.E. Wetzel, 2016
- Genus Heromphala P. Lefebure, 1947
- Genus Heroneis P. Lefebure, 1947
- Genus Himantosoma Trevisan, 1848
- Genus Humbugodiscus J. Deby, 1890
- Genus Hyalodes F. Dujardin, 1842
- Genus Hyalopyxis I.V. Makarova, 1989 †
- Genus Hylobiblium Wolle, 1894 †
- Genus Hystrix Bory de Saint-Vincent, 1822
- Genus Isomeria Chevallier
- Genus Jousea Z.I. Glezer, 1967
- Genus Kannoa S. Komura, 1980 †
- Genus Kozhowia M.S. Kulikowskiy & H. Lange-Bertalot in Kulikovskiy, Lange-Bertalot, Metzeltin & Witkowski, 2012
- Genus Ktenodiscus Pantocsek, 1889
- Genus Lobarzewskya V.B.A. Trevisan di San Leon, 1848
- Genus Lunulina Bory de Saint-Vincent, 1822
- Genus Lysicyclia Ehrenberg, 1856
- Genus Margaritoxon C. Janisch, 1862
- Genus Mediopyxis L.K. Medlin & S.F. Kühn in Kühn, Klein, Halliger, Hargraves & Medlin, 2006
- Genus Medlinella T.A. Frankovich, M.P. Ashworth & M.J. Sullivan in Frankovich et al., 2016
- Genus Melotomus Corda
- Genus Meretrosulus G.D. Hanna, 1927 †
- Genus Micrampulla G.D. Hanna, 1927 † accepted as Ktenodiscus Pantocsek, 1889
- Genus Microspodiscus Grunow, 1883
- Genus Moelleria P.T. Cleve, 1873
- Genus Monocis P. Lefebure, 1947
- Genus Monocladia I. Suto, 2003 †
- Genus Neidiomorpha H. Lange-Bertalot & M. Cantonati in Cantonati, Lange-Bertlaot & Angeli, 2010
- Genus Neomoelleria S. Blanco & C.E. Wetzel, 2016
- Genus Novilla Heiberg, 1863
- Genus Ocularia E.J. Quekett, 1844
- Genus Oncodiscus J.W. Bailey
- Genus Orthotropis Cleve, 1891
- Genus Oscillaria C. Pollini, 1816
- Genus Palmella E.A. Flint
- Genus Paltonophora Kützing, 1833
- Genus Pappia M. Hajos, 1974 †
- Genus Paradesmus A.C.J. Corda, 1835
- Genus Peragalloella H. Van Heurck, 1909
- Genus Peroniopsis F. Hustedt, 1952
- Genus Petitia M. Peragallo in Tempère & H. Peragallo, 1909 accepted as Halopetitia S. Blanco & C.E. Wetzel, 2016
- Genus Phaeothallus K.I. Meyer
- Genus Phalarina Ehrenberg
- Genus Plicatodiscus Z.I. Glezer, 1988
- Genus Polyceratium A.F. Castracane, 1886
- Genus Polymyscos C. Janisch, 1888
- Genus Ponticella Ehrenberg, 1873
- Genus Praecymatosira N.I. Strelnikova in Dzinoridze, Jousé & Stelnikova, 1979 †
- Genus Proshkinia N.I. Karayeva, 1978
- Genus Protonema Meneghini, 1845
- Genus Pseudocoscinodiscus Grunow, 1883
- Genus Pseudodiploneis A. Schmidt, 1874
- Genus Pseudohyalodiscus T.F. Kozyrenko & I.V. Makarova, 1997
- Genus Pseudomastogloia Pantocsek, 1905
- Genus Pseudoperonia E. Manguin, 1964
- Genus Pseudo-pleurosigma Cleve & Grunow, 1880
- Genus Pseudosynedra Pantocsek ex G. Moesz, 1904
- Genus Pseudotribrachia S. Blanco & C.E. Wetzel, 2016
- Genus Psygmatella Kützing, 1834
- Genus Pterotheca Grunow ex Forti, 1909 accepted as Ktenodiscus Pantocsek, 1889
- Genus Rexlowea J.P. Kociolek & E.W. Thomas, 2010
- Genus Rhaphococcus Ehrenberg, 1871
- Genus Robinsetta G.D. Hanna & A.L. Brigger, 1964 †
- Genus Salpa P. Lefebure, 1947
- Genus Scapha Edwards ex C. Johnston, 1860
- Genus Scaphularia Kützing, 1844
- Genus Sceptronema H. Takano, 1983
- Genus Schimittia P. Lefebure, 1947
- Genus Schmidtia C. Janisch, 1888 (MS)
- Genus Schumanniana P. Lefebure, 1947
- Genus Scoresbya N.I. Hendey, 1937 accepted as Hendeyscoresbya S. Blanco & C.E. Wetzel, 2016
- Genus Scytellum C.A. Agardh, 1827
- Genus Sellaphoropsis D. Metzeltin & H. Lange-Bertalot, 2002
- Genus Sembeya P. Lefebure, 1947
- Genus Sphaerotermia Ehrenberg, 1852
- Genus Stenopterotia F. Habirshaw, 1878
- Genus Stephanosira G. Karsten, 1906 accepted as Diatostephana E.A. Molinari-Novoa & M.D. Guiry, 2021
- Genus Stichostaura Ehrenberg, 1853
- Genus Stictodiscella G.B. De Toni, 1894
- Genus Stictoneis Kützing, 1844
- Genus Striatocellina Z.I. Glezer, 1988
- Genus Stylaria Hooker
- Genus Thaumaleorhabdium V.B.A. Trevisan di San Leon, 1848
- Genus Toxosira A. de Brébisson ex M. Peragallo, 1903
- Genus Vanheurckella Pantocsek †
- Genus Vavia A. Missuna, 1914 †
- Genus Vernadskowia A. Missuna, 1914 †
- Genus Weissflogia C. Janisch, 1888
- Genus Wrightia E. O'Meara, 1867
- Genus Xanthiopsis F. Wolle, 1890 †
- Class Coscinodiscophyceae
- Class Mediophyceae
- Order Bacillariophyta (awaiting allocation)
- Phylum Bigyra
- Phylum Chrysophyta accepted as Ochrophyta
- Phylum Diatomaceae accepted as Bacillariophyta
- Phylum Eustigmatophyta accepted as Ochrophyta
- Phylum Heterokontophyta accepted as Ochrophyta
- Phylum Hyphochytriomycota accepted as Pseudofungi
- Phylum Labyrinthista accepted as Bigyra
- Phylum Ochrophyta
- Phylum Oomycota accepted as Pseudofungi
- Phylum Phaeophyta accepted as Ochrophyta
- Phylum Pseudofungi
- Phylum Raphidophyta accepted as Ochrophyta
- Phylum Sagenista accepted as Bigyra
- Phylum Xanthophyta accepted as Ochrophyta
- Subphylum Bigyromonada
- Class Bigyromonadea accepted as Developea
- Family Kaonashiidae Weston, Eglit & Simpson, 2023
- Infrakingdom Rhizaria
- Kingdom Fungi
- Kingdom Plantae
- Kingdom Protista accepted as Protozoa
- Kingdom Protozoa
- Kingdom Viruses
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