Between brackets is the number of accepted species
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2 Shows the number of accepted species within the taxon
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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
- Class Coscinodiscophyceae
- Class Mediophyceae
- Order Anaulales
- Order Biddulphiales
- Order Bilinguales †
- Order Briggerales
- Order Chaetocerotales
- Order Climacospheniales accepted as Toxariales
- Order Cymatosirales
- Order Eupodiscales
- Family Eupodiscaceae Kützing, 1849
- Genus Amphipentas Ehrenberg, 1840 †
- Genus Auliscus Ehrenberg, 1843
- Genus Cerataulus Ehrenberg, 1844
- Genus Debya J. Rattray, 1888 accepted as Rattrayella G.B. De Toni, 1889
- Species Debya oamaruensis (Grunow) Rattray accepted as Rattrayella oamaruensis (Grunow) De Toni
- Genus Entogoniopsis P.A. Sims, N.I. Strelnikova, J. Witkowski & D.M. Williams in Witkowski et al., 2015
- Genus Eupodiscus J.W. Bailey, 1851
- Genus Hobaniella P.A. Sims & D.M. Williams in Sims et al., 2018
- Genus Mastodiscus J.W. Bailey, 1854
- Genus Noszkya P. Lefébure & E. Chenevière, 1939 †
- Genus Pleurosira (G. Meneghini) V.B.A. Trevisan, 1848
- Genus Pseudauliscus A. Schmidt, 1875
- Genus Pseudoauliscus accepted as Pseudauliscus A. Schmidt, 1875
- Genus Rattrayella G.B. De Toni, 1889
- Genus Sextiputeus R. Ross & P.A. Sims, 2000 †
- Genus Trilamina P.A. Sims, N.I. Strelnikova, J. Witkowski & D.M. Williams in Witkowski et al., 2015 †
- Genus Xystotheca G.D. Hanna, 1932 †
- Genus Zygoceros C.G. Ehrenberg, 1839
- Family Odontellaceae P.A. Sims, D.M. Williams & M. Ashworth, 2018
- Family Parodontellaceae †
- Order Hemiaulales
- Order Leptocylindrales accepted as Chaetocerotales
- Order Lithodesmiales
- Order Stephanodiscales
- Order Thalassiosirales
- Order Toxariales
- Order Triceratiales
- 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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