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
- Order Cyttariales
- Order Erysiphales
- Order Helotiales
- Family Amicodiscaceae A.H. Ekanayaka & K.D. Hyde in Ekanayaka, Hyde, Gentekaki, McKenzie, Zhao, Bulgakov & Camporesi, 2019
- Family Arachnopezizaceae T. Hosoya, J.G. Han & H.O. Baral in Baral, 2015
- Family Ascocorticiaceae
- Family Bryoglossaceae A.H. Ekanayaka & K.D. Hyde in Ekanayaka, Hyde, Gentekaki, McKenzie, Zhao, Bulgakov & Camporesi, 2019
- Family Chlorociboriaceae H.O. Baral & P.R. Johnston in Baral, 2015
- Family Chlorospleniaceae A.H. Ekanayaka & K.D. Hyde in Ekanayaka, Hyde, Gentekaki, McKenzie, Zhao, Bulgakov & Camporesi, 2019
- Family Dermateaceae
- Family Discinellaceae A.H. Ekanayaka & K.D. Hyde in Ekanayaka, Hyde, Gentekaki, McKenzie, Zhao, Bulgakov & Camporesi, 2019
- Family Excipulaceae accepted as Helotiales incertae sedis
- Family Hamatocanthoscyphaceae A.H. Ekanayaka & K.D. Hyde, 2019
- Family Helotiaceae
- Family Helotiales incertae sedis
- Family Hemiphacidiaceae
- Family Hyaloscyphaceae
- Family Hydrocinaceae A.H. Ekanayaka & K.D. Hyde in Ekanayaka, Hyde, Gentekaki, McKenzie, Zhao, Bulgakov & Camporesi, 2019
- Family Hymenoscyphaceae accepted as Helotiaceae
- Family Loramycetaceae
- Family Mollisiaceae accepted as Helotiales incertae sedis
- Family Moniliaceae accepted as Sclerotiniaceae
- Family Neolauriomycetaceae P.W. Crous in Crous et al., 2018
- Family Patellariopsidaceae A. Karunarathna, E. Camporesi & K.D. Hyde in Karunarathna et al., 2020
- Family Pezizellaceae J. Velenovský, 1934
- Family Phacidiaceae
- Family Rhizothyriaceae accepted as Helotiaceae
- Family Rutstroemiaceae
- Family Sclerotiniaceae
- Genus Acarosporium Bubák & Vleugel ex Bubák, 1911
- Genus Amerosporina (Petrak) Petrak, 1965 accepted as Amerosporium Spegazzini, 1882
- Genus Amerosporium Spegazzini, 1882
- Genus Amphobotrys G.L. Hennebert, 1973
- Genus Asterobolus Redhead & P.W. Perrin, 1972 accepted as Valdensia B. Peyronel, 1923
- Genus Asterocalyx F. von Höhnel, 1912
- Genus Botryophialophora Linder, 1944
- Genus Botryotinia Whetzel, 1945
- Genus Botrytis P. Micheli ex Persoon, 1794
- Genus Cephalocladium H.G.L. Reichenbach, 1829 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Chaetalysis Peyronel, 1922 accepted as Acarosporium Bubák & Vleugel ex Bubák, 1911
- Genus Ciboria Fuckel, 1870
- Genus Ciborinia H.H. Whetzel, 1945
- Genus Ciboriopsis Dennis, 1962 accepted as Ciboria Fuckel, 1870
- Genus Ciliosira H. Sydow, 1942 accepted as Acarosporium Bubák & Vleugel ex Bubák, 1911
- Genus Coccotrichum Link in Willdenow, 1824 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Cristularia (P.A. Saccardo) J. Costantin, 1888 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Cristulariella F. von Höhnel, 1916
- Genus Cudoniopsis Spegazzini, 1925
- Genus Dumontinia L.M. Kohn, 1979
- Genus Elliottinia L.M. Kohn, 1979
- Genus Encoelia (E.M. Fries) P.A. Karsten, 1871
- Genus Encoeliopsis Kirschstein, 1935
- Genus Epochnium Link, 1809 accepted as Monilia Bonorden, 1851
- Genus Gonatobotrytites Pia in M. Hirmer, 1927 †
- Genus Grovesinia M.N. Cline, J.L. Crane & S.D. Cline, 1983
- Genus Halobyssus H. Zukal, 1893 accepted as Monilia Bonorden, 1851
- Genus Haplaria Link in Willdenow, 1824 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Hinomyces Narumi & Y. Harada, 2006
- Genus Kohninia A. Holst-Jensen, T. Vrålstad & T. Schumacher, 2004
- Genus Lambertellinia Korf & Lizon, 1994
- Genus Martinia Whetzel, 1942 accepted as Martininia K.P. Dumont & R.P. Korf, 1970
- Genus Martininia K.P. Dumont & R.P. Korf, 1970
- Genus Membranatheca T. Matsushima, 1995 accepted as Amerosporium Spegazzini, 1882
- Genus Mitrulinia B.M. Spooner, 1987
- Genus Moellerodiscus Hennings, 1902 accepted as Ciboria Fuckel, 1870
- Genus Monilia Bonorden, 1851
- Genus Monilia Link, 1809 accepted as Monilia Bonorden, 1851
- Genus Monilia Hill ex F.H. Wiggers, 1780 accepted as Monilia Bonorden, 1851
- Genus Monilinia E.E. Honey, 1928
- Genus Monilites L. Pampaloni, 1902 †
- Genus Moserella R. Pöder & C. Scheuer, 1994
- Genus Mycopappus S.A. Redhead & G.P. White, 1985
- Genus Myrioconium H. Sydow, 1912
- Genus Myriosclerotinia N.F. Buchwald, 1947
- Genus Nervostroma Narumi & Y. Harada, 2006
- Genus Ocellaria (Tulasne & C. Tulasne) Kirschstein, 1935
- Genus Ovulinia F.A. Weiss, 1940
- Genus Ovulitis N.F. Buchwald, 1970 accepted as Ovulinia F.A. Weiss, 1940
- Genus Penecillium accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Penicillium E.M. Fries, 1832 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Phaeangella (P.A. Saccardo) G. Massee, 1895 accepted as Encoelia (E.M. Fries) P.A. Karsten, 1871
- Genus Phaeopolynema (Spegazzini) Petrak & Sydow, 1937
- Genus Phaeosclerotinia S. Hori, 1916
- Genus Phibalis Wallroth, 1833 accepted as Encoelia (E.M. Fries) P.A. Karsten, 1871
- Genus Phymatotrichum Bonorden, 1851 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Piceomphale M. Svrček, 1957 accepted as Ciboria Fuckel, 1870
- Genus Pleurobotrya Berkeley accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Poculinia B.M. Spooner, 1987
- Genus Polyactis Link, 1809 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Pseudociboria Kanouse, 1944
- Species Pseudociboria umbrina Kanouse, 1944
- Genus Pterodinia Chevallier, 1837 accepted as Botrytis P. Micheli ex Persoon, 1794
- Genus Pycnopeziza W.L. White & H.H. Whetzel, 1938
- Genus Ramularites Pia in M. Hirmer, 1927 †
- Genus Redheadia Y. Suto & Suyama, 2005
- Genus Rhacodiella B. Peyronel, 1919 accepted as Myrioconium H. Sydow, 1912
- Genus Sclerocrana G.J. Samuels & L.M. Kohn, 1987
- Genus Sclerotinia Fuckel, 1870
- Genus Seaverinia Whetzel, 1945
- Genus Septotinia Whetzel, 1937
- Genus Septotinia Whetzel ex J.W. Groves & M.E. Elliott, 1961
- Genus Septotis N.F. Buchwald ex Arx, 1970
- Genus Streptobotrys G.L. Hennebert, 1973
- Genus Streptotinia Whetzel, 1945
- Genus Stromatinia (Boudier) Boudier, 1907
- Genus Thyriochaetum I.P. Frolov, 1968 accepted as Amerosporium Spegazzini, 1882
- Genus Torrendiella Boudier & Torrend, 1911
- Genus Valdensia B. Peyronel, 1923
- Genus Valdensinia Peyronel, 1953
- Genus Verrucobotrys G.L. Hennebert, 1973
- Genus Whetzelinia Korf & K.P. Dumont, 1972 accepted as Sclerotinia Fuckel, 1870
- Genus Zoellneria Velenovský, 1934 accepted as Torrendiella Boudier & Torrend, 1911
- Family Solenopeziaceae A.H. Ekanayaka & K.D. Hyde in Ekanayaka, Hyde, Gentekaki, McKenzie, Zhao, Bulgakov & Camporesi, 2019
- Family Tympanidaceae H.O. Baral & L. Quijada in Baral, 2015
- Family Vandijckellaceae M. Sandoval-Denis in Crous et al., 2017
- Family Vibrisseaceae
- Order Leotiales
- Order Leotiomycetes incertae sedis
- Order Leotiomycetidae incertae sedis
- Order Lichinodiales
- Order Medeolariales
- Order Rhytismatales
- Order Thelebolales
- 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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