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
- Kingdom Fungi
- Phylum Aphelida accepted as Aphelidiomycota
- Phylum Aphelidiomycota
- Phylum Ascomycota
- Class Archaeorhizomycetes
- Class Arthoniomycetes
- Class Ascomycetes
- Class Ascomycota incertae sedis
- Class Ascomycotina incertae sedis
- Class Dothideomycetes
- Order Abrothallales
- Order Acrospermales
- Order Arthrocatenales
- Order Asterinales
- Order Bezerromycetales accepted as Tubeufiales
- Order Botryosphaeriales
- Order Capnodiales
- Order Catinellales
- Order Cladoriellales
- Order Collemopsidiales
- Order Coniosporiales
- Order Dothideales
- Order Dothideomycetes incertae sedis
- Order Dothideomycetidae incertae sedis
- Family Argynnaceae Shearer & J.L. Crane, 1980
- Family Ascoporiaceae Kutorga & D. Hawksworth, 1997
- Family Dimeriaceae E. Müller & Arx ex Arx & E. Müller, 1975
- Family Dothideomycetidae incertae sedis
- Family Hypsostromataceae Huhndorf, 1994
- Family Micropeltaceae † accepted as Micropeltidaceae
- Family Micropeltidaceae
- Family Microtheliopsidaceae
- Family Moriolaceae
- Family Munkiellaceae (Theissen & Sydow) Luttrell, 1973 accepted as Polystomellaceae Theissen & Sydow, 1915
- Family Mycoporaceae
- Family Parodiopsidaceae
- Family Phillipsiellaceae
- Family Polystomellaceae Theissen & Sydow, 1915
- Genus Apiotrabutia Petrak, 1929 accepted as Munkiella Spegazzini, 1885
- Genus Coscinopeltis Spegazzini, 1909 accepted as Munkiella Spegazzini, 1885
- Species Coscinopeltis tenuis (Speg.) Theiss. & Syd., 1915 accepted as Munkiella caa-guazu Speg., 1885
- Genus Dermatodothella Viégas, 1944
- Genus Dothidella Spegazzini, 1880
- Genus Dothithyriella F. von Höhnel, 1918
- Genus Hypostigme H. Sydow, 1925 accepted as Parastigmatea Doidge, 1921
- Genus Marchalia P.A. Saccardo, 1889
- Genus Munkiella Spegazzini, 1885
- Genus Parastigmatea Doidge, 1921
- Genus Pluriporus F.L. Stevens & Ryan in F.L. Stevens, 1925 accepted as Dothidella Spegazzini, 1880
- Genus Polystomella Spegazzini, 1888 accepted as Dothidella Spegazzini, 1880
- Family Saccardiaceae
- Family Vizellaceae H.J. Swart, 1971
- Order Dyfrolomycetales
- Order Eremithallales
- Order Eremomycetales
- Order Hysteriales
- Order Jahnulales
- Order Kirschsteiniotheliales
- Order Koralionastetales
- Order Lembosinales
- Order Lichenotheliales
- Order Meliolales
- Order Microthyriales
- Order Minutisphaerales
- Order Monoblastiales
- Order Murramarangomycetales
- Order Muyocopronales
- Order Myriangiales
- Order Mytilinidiales
- Order Natipusillales
- Order Neodactylariales
- Order Parmulariales
- Order Patellariales
- Order Phaeotrichales
- Order Pleosporales
- Order Stigmatodiscales
- Order Strigulales
- Order Superstratomycetales
- Order Trypetheliales
- Order Tubeufiales
- Order Valsariales
- Order Venturiales
- Order Wiesneriomycetales accepted as Tubeufiales
- Order Zeloasperisporiales
- Class Eurotiomycetes
- Class Geoglossomycetes
- Class Laboulbeniomycetes
- Class Lecanoromycetes
- Class Leotiomycetes
- Class Lichinomycetes
- Class Neolectomycetes
- Class Orbiliomycetes
- Class Pezizomycetes
- Class Pneumocystidomycetes
- Class Saccharomycetes
- Class Sareomycetes
- Class Schizosaccharomycetes
- Class Sordariomycetes
- Class Taphrinomycetes
- Class Xylonomycetes
- Phylum Basidiobolomycota accepted as Zygomycota
- Phylum Basidiomycota
- Phylum Blastocladiomycota
- Phylum Calcarisporiellomycota accepted as Zygomycota
- Phylum Caulochytriomycota accepted as Chytridiomycota
- Phylum Chytridiomycota
- Phylum Entomophthoromycota
- Phylum Fungi (awaiting allocation)
- Phylum Fungi incertae sedis
- Phylum Glomeromycota
- Phylum Kickxellomycota accepted as Zygomycota
- Phylum Monoblepharomycota accepted as Chytridiomycota
- Phylum Mortierellomycota accepted as Zygomycota
- Phylum Mucoromycota accepted as Zygomycota
- Phylum Nematophyta †
- Phylum Neocallimastigomycota accepted as Chytridiomycota
- Phylum Olpidiomycota accepted as Chytridiomycota
- Phylum Rozellomycota
- Phylum Zoopagomycota accepted as Zygomycota
- Phylum Zygomycota
- Genus Celluloxylon J.W. Dawson, 1881 † accepted as Prototaxites J.W. Dawson, 1859 †
- Genus Mucorites Meschinelli, 1898 † accepted as Mucorites Meschinelli ex Lindau, 1900 †
- Genus Mucorites Meschinelli ex Lindau, 1900 †
- Genus Mycelites W. Roux, 1887 †
- Genus Mycobystrovia Goujet & Locquin, 1979 †
- Genus Nematophycus Carruthers, 1872 † accepted as Prototaxites J.W. Dawson, 1859 †
- Genus Nematophyton J.W. Dawson, 1888 † accepted as Prototaxites J.W. Dawson, 1859 †
- Genus Ourasphaira C.C. Loron, R.H. Rainbird, E.C. Turner, J.W. Greenman & E.J. Javaux, 2019 †
- Genus Petsamomyces M.Y. Belova, 2006 †
- Genus Pilula S.D. Harker & W.A.S. Sarjeant in Harker et al., 1990 † accepted as Pilula S.D. Harker & W.A.S. Sarjeant ex S.D. Harker & W.A.S. Sarjeant, 1992 †
- Genus Pilula S.D. Harker & W.A.S. Sarjeant ex S.D. Harker & W.A.S. Sarjeant, 1992 †
- Genus Polycellaria H.D. Pflug, 1965 †
- Genus Prototaxites J.W. Dawson, 1859 †
- Genus Rhyniomycelium M. Krings & C.J. Harper, 2023 †
- Kingdom Plantae
- Kingdom Protista accepted as Protozoa
- Kingdom Protozoa
- Kingdom Viruses
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