Between brackets is the number of accepted species
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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
- 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
- Order Amphisphaeriales
- Order Annulatascales
- Order Boliniales
- Order Calosphaeriales
- Order Cancellidiales
- Order Chaetosphaeriales
- Order Coniochaetales
- Order Coronophorales
- Order Diaporthales
- Order Hypocreales
- Order Hypocreomycetidae incertae sedis
- Order Jobellisiales
- Order Lulworthiales
- Order Melanosporales
- Order Microascales
- Order Ophiostomatales
- Order Phomatosporales
- Order Phyllachorales
- Order Sordariales
- Order Sordariomycetes incertae sedis
- Order Sordariomycetidae incertae sedis
- Order Tirisporellales
- Order Trichosphaeriales
- Order Xylariales
- Family Appendicosporaceae M.C. Samarakoon & K.D. Hyde in Samarakoon et al., 2022
- Family Cainiaceae J.C.Krug, 1978
- Family Clypeosphaeriaceae
- Family Diatrypaceae Nitschke, 1869
- Genus Allodiatrype S. Konta & K.D. Hyde, 2020
- Genus Anthostoma Nitschke, 1867 accepted as Cryptosphaeria Cesati & De Notaris, 1853
- Genus Anthostoma von Höhnel, 1912
- Genus Cladosphaeria Nitschke ex Jaczewski, 1894 accepted as Cryptosphaeria Cesati & De Notaris, 1853
- Genus Cryptosphaeria Cesati & De Notaris, 1853
- Species Cryptosphaeria mangrovei K.D. Hyde, 1993
- Genus Cryptosphaerina Lambotte & Fautrey ex P.A. Saccardo & P. Sydow, 1902 accepted as Cryptosphaeria Cesati & De Notaris, 1853
- Genus Diatrypasimilis J.J. Zhou & J. Kohlmeyer, 2010 accepted as Diatrypasimilis J.J. Zhou & J. Kohlmeyer in S.-O. Suh, 2016
- Genus Diatrypasimilis J.J. Zhou & J. Kohlmeyer in S.-O. Suh, 2016
- Genus Diatrype E.M. Fries, 1849
- Genus Diatrypella (Cesati & De Notaris) De Notaris, 1863
- Genus Dothideovalsa Spegazzini, 1909
- Genus Echinomyces F. Rappaz, 1987
- Genus Ectosphaeria Spegazzini, 1921 accepted as Diatrype E.M. Fries, 1849
- Genus Endoxylina Romell, 1892
- Genus Epheliopsis Hennings, 1908 accepted as Eutypa L.R. Tulasne & C. Tulasne, 1863
- Genus Eutypa L.R. Tulasne & C. Tulasne, 1863
- Genus Eutypella (Nitschke) P.A. Saccardo, 1875
- Genus Fassia R.W.G. Dennis, 1964
- Genus Lageniformia Plunkett, 1925 accepted as Eutypa L.R. Tulasne & C. Tulasne, 1863
- Genus Leptoperidia F. Rappaz, 1987
- Genus Melanostictus M.C. Samarakoon & K.D. Hyde in Samarakoon et al., 2022
- Genus Monosporascus F.G. Pollack & F.A. Uecker, 1974
- Genus Paraeutypa C.V. Subramanian & D. Ananthapadmanaban, 1988 accepted as Leptoperidia F. Rappaz, 1987
- Genus Peroneutypa Berlese, 1902 accepted as Eutypella (Nitschke) P.A. Saccardo, 1875
- Genus Peroneutypella Berlese, 1902 accepted as Eutypella (Nitschke) P.A. Saccardo, 1875
- Genus Phaeotrype P.A. Saccardo, 1920 accepted as Diatrype E.M. Fries, 1849
- Genus Pogonospora Petrak, 1957 accepted as Endoxylina Romell, 1892
- Genus Pseudoeutypa S.N. Zhang & E.B.G. Jones, 2024
- Genus Pseudotrype P.C. Hennings, 1900 accepted as Eutypella (Nitschke) P.A. Saccardo, 1875
- Genus Pyrenodochium H.F. Bonorden, 1851 accepted as Diatrype E.M. Fries, 1849
- Genus Quaternaria L.R. Tulasne & C. Tulasne, 1863 accepted as Eutypella (Nitschke) P.A. Saccardo, 1875
- Genus Quoternia
- Genus Rostronitschkia Fitzpatrick, 1919
- Genus Scoptria Nitschke, 1867 accepted as Eutypella (Nitschke) P.A. Saccardo, 1875
- Genus Sphaerosperma Preuss, 1853 accepted as Diatrypella (Cesati & De Notaris) De Notaris, 1863
- Genus Stictosphaeria L.R. Tulasne & C. Tulasne, 1863 accepted as Diatrype E.M. Fries, 1849
- Genus Stigmatopsis J.B. Traverso, 1906 accepted as Cryptosphaeria Cesati & De Notaris, 1853
- Genus Stromatolinea K. Habib & Q.R. Li, 2024
- Genus Tilakomyces Sathe & J.G. Vaidya in J.G. Vaidya, 1979 accepted as Eutypella (Nitschke) P.A. Saccardo, 1875
- Genus Valsa Adanson, 1763 accepted as Diatrype E.M. Fries, 1849
- Family Graphostromataceae
- Family Hemisphaeriaceae accepted as Xylariaceae
- Family Hyponectriaceae
- Family Iodosphaeriaceae
- Family Microdochiaceae M. Hernández-Restrepo, J.Z. Groenewald & P.W. Crous, 2016
- Family Myelospermataceae
- Family Sphaeriaceae accepted as Xylariaceae
- Family Vamsapriyaceae Y.R. Sun, Y. Wang bis & K.D. Hyde, 2021
- Family Xylariaceae
- Family Xylariales incertae sedis
- Order Xylariomycetidae incertae sedis
- 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 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 Ourasphaira C.C. Loron, R.H. Rainbird, E.C. Turner, J.W. Greenman & E.J. Javaux, 2019 †
- Genus Rhyniomycelium M. Krings & C.J. Harper, 2023 †
- Genus Tappania Yin, 1997 †
- Kingdom Plantae
- Kingdom Protista accepted as Protozoa
- Kingdom Protozoa
- Kingdom Viruses
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