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
- 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
- Family Amphipleuraceae Grunow, 1862
- Family Amphiraphiaceae accepted as Naviculaceae Kützing, 1844
- Family Berkeleyaceae Mann
- Family Brachysiraceae Mann, 1990
- Family Cavinulaceae D.G. Mann
- Family Cosmioneidaceae D. G. Mann
- Family Diadesmidaceae D.G. Mann in Round et al., 2000
- Genus Diadesmis Kützing, 1844
- Genus Humidophila (Lange-Bertalot & Werum) R.L. Lowe, P. Kociolek, J.R. Johansen, B. Van de Vijver, H. Lange-Bertalot & K. Kopalová, 2014
- Genus Luticola D.G. Mann in F.E. Round, R.M. Crawford & D.G. Mann, 1990
- Genus Paraluticola D. Metzeltin & H. Lange-Bertalot, 2002
- Family Diploneidaceae D. G. Mann, 1990
- Family Metascolioneidaceae S. Blanco & C.E. Wetzel, 2016
- Family Naviculaceae Kützing, 1844
- Family Naviculales (awaiting allocation)
- Family Neidiaceae Mersechkkowsky, 1903
- Family Phaeodactylaceae Silva, 1962
- Family Pinnulariaceae D.G. Mann, 1990
- Family Plagiotropidaceae D. G. Mann
- Family Pleurosigmataceae Mereschkowsky, 1903
- Family Proschkiniaceae D. G. Mann
- Family Psycheneidaceae
- Family Scolioneidaceae D.G. Mann, 1990 accepted as Metascolioneidaceae S. Blanco & C.E. Wetzel, 2016
- Family Scoliotropidaceae K.S. Mereschkowski, 1903
- Family Sellaphoraceae Mereschkowsky, 1902
- Family Stauroneidaceae D.G. Mann, 1990
- Genus Lutophila S. Kheiri, M.A. Edlund, S. Spaulding & C.E. Solak in Kerhi et al., 2024
- 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
- 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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