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
- Family Bionectriaceae
- Family Clavicipitaceae (Lindau) Earle, 1901
- Family Cordycipitaceae Kreisel ex G.H. Sung, J.M. Sung, Hywel-Jones & Spatafora, 2007
- Family Hypocreaceae
- Genus Aleurisma Link, 1809 accepted as Trichoderma Persoon, 1794
- Genus Aphysiostroma J.M. Barrasa, A.T. Martínez & G. Moreno, 1986
- Genus Apiocrea H. Sydow & P. Sydow, 1921 accepted as Hypomyces (E.M. Fries) L.R. Tulasne, 1860
- Genus Arachnocrea Z. Moravec, 1956
- Genus Arnoldia D.J. Gray & G. Morgan-Jones, 1980 accepted as Arnoldiomyces G. Morgan-Jones, 1980
- Genus Arnoldiomyces G. Morgan-Jones, 1980
- Genus Asterothecium F.G. Wallroth, 1836 accepted as Stephanoma Wallroth, 1833
- Genus Bonordenia S. Schulzer von Müggenburg in S. Schulzer von Müggenburg, Kanitz & Knapp, 1866 accepted as Hypomyces (E.M. Fries) L.R. Tulasne, 1860
- Genus Chiajaea (P.A. Saccardo) F. von Höhnel, 1920 accepted as Hypomyces (E.M. Fries) L.R. Tulasne, 1860
- Genus Chromocrea Seaver, 1910 accepted as Hypocrea E.M. Fries, 1825
- Genus Cladobotryum C.G.D. Nees ex Brongniart in F. Cuvier, 1824
- Genus Clintoniella (P.A. Saccardo) Rehm, 1900 accepted as Hypomyces (E.M. Fries) L.R. Tulasne, 1860
- Genus Coccosporella P.A. Karsten, 1893 accepted as Mycogone Link, 1809
- Genus Corymbomyces O. Appel & Strunk, 1904 accepted as Gliocladium Corda, 1840
- Genus Creopus Link, 1833 accepted as Hypocrea E.M. Fries, 1825
- Genus Debarya S. Schulzer von Müggenburg in S. Schulzer von Müggenburg, Kanitz & Knapp, 1866 accepted as Hypocrea E.M. Fries, 1825
- Genus Dialhypocrea Spegazzini, 1919
- Genus Didymocladium P.A. Saccardo, 1886 accepted as Cladobotryum C.G.D. Nees ex Brongniart in F. Cuvier, 1824
- Genus Diplocladium Bonorden, 1851 accepted as Cladobotryum C.G.D. Nees ex Brongniart in F. Cuvier, 1824
- Genus Dozya P.A. Karsten, 1873 accepted as Hypocreopsis P.A. Karsten, 1873
- Genus Escovopsioides H.C. Evans & J.O. Augustin in Augustin, Groenewald, Nascimento, Mizubuti, Barreto, Elliot & Evans, 2013
- Genus Gliocladium Corda, 1840
- Genus Hyphomyces C.H. Bridges & C.W. Emmons, 1961
- Genus Hypocrea E.M. Fries, 1825
- Genus Hypocreopsis P.A. Karsten, 1873
- Species Hypocreopsis hypoxyloides Speg., 1899 accepted as Valsaria rubricosa (Fr.) Sacc., 1876
- Species Hypocreopsis lichenoides (Tode) Seaver, 1910
- Species Hypocreopsis macrostoma (Berk. & M.A. Curtis) E. Müll., 1962 accepted as Nectria macrostoma Berk. & M.A. Curtis, 1868
- Species Hypocreopsis phyllostachydis (Syd.) I. Miyake & Hara, 1910 accepted as Mycocitrus phyllostachydis (Syd.) Yoshim. Doi, 1967
- Species Hypocreopsis pulchra G. Winter, 1875 accepted as Selinia pulchra (G. Winter) Sacc., 1883
- Species Hypocreopsis rhododendri Thaxt., 1922
- Species Hypocreopsis riccioidea (Bolton) P. Karst., 1871 accepted as Hypocreopsis lichenoides (Tode) Seaver, 1910
- Species Hypocreopsis tremellicola (Ellis & Everh.) Seaver, 1910 accepted as Nectriopsis tremellicola (Ellis & Everh.) W. Gams, 1982
- Species Hypocreopsis tuberculariformis (Rehm) Sacc., 1891 accepted as Nectria tuberculariformis (Rehm ex Sacc.) G. Winter
- Genus Hypomyces (E.M. Fries) L.R. Tulasne, 1860
- Genus Lecithium P.A. Saccardo, 1895
- Genus Leiosepium P.A. Saccardo in P.A. Saccardo & Fautrey, 1900 accepted as Sepedonium Link, 1809
- Genus Luteomyces Q.V. Montoya & A. Rodrigues, 2021
- Genus Miyakeamyces K. Hara, 1913
- Genus Mucrosporium Preuss, 1851 accepted as Cladobotryum C.G.D. Nees ex Brongniart in F. Cuvier, 1824
- Genus Mycobanche Persoon, 1818 accepted as Mycogone Link, 1809
- Genus Mycogone Link, 1809
- Genus Pachybasium P.A. Saccardo, 1885 accepted as Trichoderma Persoon, 1794
- Genus Peckiella (P.A. Saccardo) P.A. Saccardo, 1891 accepted as Hypomyces (E.M. Fries) L.R. Tulasne, 1860
- Genus Podocrea (P.A. Saccardo) Lindau in Engler & Prantl, 1897 accepted as Podostroma P.A. Karsten, 1892
- Genus Podostroma P.A. Karsten, 1892
- Genus Protocrea Petch, 1937
- Genus Pseudohypocrea Y. Doi, 1972
- Genus Pyreniopsis O. Kuntze, 1898 accepted as Trichoderma Persoon, 1794
- Genus Pyrenium Tode, 1790 accepted as Trichoderma Persoon, 1794
- Genus Rogersonia G.J. Samuels & D.J. Lodge, 1996
- Genus Sarawakus Lloyd, 1924
- Genus Sepedonium Link, 1809
- Genus Sibirina G.R.W. Arnold, 1970
- Genus Sphaerostilbella (Hennings) P.A. Saccardo & D. Saccardo, 1905
- Genus Sporoderma Montagne, 1856 accepted as Trichoderma Persoon, 1794
- Genus Sporophagomyces K. Pöldmaa & G.J. Samuels in K. Pöldmaa et al., 2000
- Genus Stephanoma Wallroth, 1833
- Genus Sympodiorosea Q.V. Montoya & A. Rodrigues, 2021
- Genus Synthetospora A.P. Morgan, 1892 accepted as Stephanoma Wallroth, 1833
- Genus Tilakidium J.G. Vaidya, C.D. Naik & M.M. Rathod, 1986
- Genus Tolypomyria Preuss, 1852 accepted as Trichoderma Persoon, 1794
- Genus Trichoderma Persoon ex Gray, 1801
- Genus Trichoderma Persoon, 1794
- Genus Verticilliastrum Daszewska, 1912 accepted as Trichoderma Persoon, 1794
- Family Hypocreales incertae sedis
- Family Nectriaceae
- Family Niessliaceae
- Family Ophiocordycipitaceae G.H. Sung, J.M. Sung, Hywel-Jones & Spatafora, 2007 accepted as Cordycipitaceae Kreisel ex G.H. Sung, J.M. Sung, Hywel-Jones & Spatafora, 2007
- Family Polycephalomycetaceae Y.P. Xiao, Y.B. Wang, T.C. Wen, H. Yu & K.D. Hyde, 2023
- Family Stilbellaceae accepted as Hypocreales incertae sedis
- Family Tuberculariaceae accepted as Nectriaceae
- Order Hypocreomycetidae incertae sedis
- Order Jobellisiales
- Order Lulworthiales
- Order Melanosporales
- Order Microascales
- Order Ophiostomatales
- Order Phomatosporales
- Order Phyllachorales
- Order Pisorisporiales
- Order Sordariales
- Order Sordariomycetes incertae sedis
- Order Sordariomycetidae incertae sedis
- Order Tirisporellales
- Order Trichosphaeriales
- Order Xylariales
- 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 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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