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
- Family Alinaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Aspidotheliaceae
- Family Atichiaceae accepted as Seuratiaceae
- Family Aulographaceae Luttrell ex P.M. Kirk et al., 2001
- Family Balladynaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Brefeldiellaceae accepted as Trichopeltinaceae A.C. Batista, A.A. Costa & R. Ciferri, 1958
- Family Cleistosphaeraceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Coccoideaceae P. Hennings ex Saccardo & D. Saccardo, 1905
- Family Cookellaceae F.X.R. von Höhnel ex Saccardo & Trotter, 1885
- Family Diporothecaceae
- Family Dothideomycetes incertae sedis
- Family Dubujianaceae D. Pem, M. Doilom & K.D. Hyde in Pem et al., 2019
- Family Dysrhynchaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Endosporiaceae D. Pem, M. Doilom & K.D. Hyde in Pem et al., 2019
- Family Englerulaceae P. Hennings, 1904
- Family Eoterfeziaceae
- Family Epigloeaceae
- Family Homortomycetaceae K.M. Thambugala, A.J.L. Phillips & K.D. Hyde, 2016
- Family Hyalomeliolinaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Lautosporaceae
- Family Leptopeltidaceae von Höhnel ex Trotter, 1928
- Family Macrovalsariaceae D. Pem, M. Doilom & K.D. Hyde in Pem et al., 2019
- Family Mastodiaceae
- Family Meliolinaceae S. Hughes, 1993
- Family Mesnieraceae Arx & Müller, 1975
- Family Microglaenaceae accepted as Thelenellaceae
- Family Myxotrichaceae
- Family Naetrocymbaceae R.C. Harris, 1995
- Family Nematotheciaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Neoparodiaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Palawaniaceae A. Mapook & K.D. Hyde in Mapook et al., 2016
- Family Paranectriellaceae S. Boonmee & K.D. Hyde in Hyde et al., 2013
- Family Parodiellaceae Theissen & Sydow ex M.E. Barr, 1987
- Family Peltasteraceae accepted as Dothideomycetes incertae sedis
- Family Perisporiopsidaceae E. Müller & J.A. von Arx ex R. Kirschner & T.A. Hofmann, 2012
- Family Phaeodimeriellaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Phaneromycetaceae
- Family Pododimeriaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Polyclypeolinaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Protoscyphaceae Kutorga & D. Hawksworth, 1997
- Family Protothelenellaceae
- Genus Gloeopyrenia Zschacke in Keissler, 1937 accepted as Protothelenella Räsänen, 1943
- Genus Mycowinteria M.A. Sherwood-Pike & J.R. Boise, 1986
- Genus Protothelenella Räsänen, 1943
- Species Protothelenella corrosa (Körb.) H. Mayrhofer & Poelt, 1985
- Species Protothelenella leucothelia (Nyl.) H. Mayrhofer & Poelt, 1985
- Species Protothelenella reducta (Th. Fr.) Räsänen, 1943 accepted as Protothelenella sphinctrinoides (Nyl.) H. Mayrhofer & Poelt, 1985
- Species Protothelenella sphinctrinoidella (Nyl.) H. Mayrhofer & Poelt, 1985
- Species Protothelenella sphinctrinoides (Nyl.) H. Mayrhofer & Poelt, 1985
- Genus Winteria (Rehm) P.A. Saccardo, 1883 accepted as Mycowinteria M.A. Sherwood-Pike & J.R. Boise, 1986
- Family Pseudeurotiaceae
- Family Pseudoperisporiaceae Toro, in Seaver & Palacios Chardon, 1926
- Family Pseudorobillardaceae P.W. Crous in Crous et al., 2019
- Family Pyrenidiaceae A. Zahlbruckner in Engler, 1898
- Family Pyrenothricaceae
- Family Pyrenotrichaceae accepted as Pyrenothricaceae
- Family Roesleriaceae
- Family Seuratiaceae
- Family Seynesiopeltidaceae K.D. Hyde in Hyde et al., 2013
- Family Stomatogenaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Stomatogeneceae accepted as Stomatogenaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Thelenellaceae
- Family Thrombiaceae
- Family Thyrinulaceae X.Y. Zeng, S. Hongsanan & K.D. Hyde, 2020
- Family Toroaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Trichopeltinaceae A.C. Batista, A.A. Costa & R. Ciferri, 1958
- Family Trichothyriaceae Theissen, 1914
- Order Dothideomycetidae incertae sedis
- 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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