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
- Family Hypocreales incertae sedis
- Family Nectriaceae
- Genus Acontiopsis A. Negru, 1961 accepted as Calonectria De Notaris, 1867
- Genus Actinostilbe Petch, 1925
- Genus Albonectria Rossman & Samuels, 1999
- Genus Allantonectria Earle, 1901 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Allantospora Wakker, 1895 accepted as Cylindrocarpon H.W. Wollenweber, 1913
- Genus Allonectella Petrak, 1950
- Genus Antenaglium F.C. Albuquerque, 1969 accepted as Gliocephalotrichum J.J. Ellis & C.W. Hesseltine, 1962
- Genus Antipodium K.A. Pirozynski, 1974
- Genus Aphanocladium W. Gams, 1971
- Genus Aponectria (P.A. Saccardo) P.A. Saccardo, 1883 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Bacillispora S. Nilsson, 1962
- Genus Baipadisphaeria U. Pinruan in Pinruan et al., 2010
- Genus Bidenticula F.C. Deighton, 1972 accepted as Fusarium Link, 1809
- Genus Botryocrea Petrak, 1949 accepted as Fusarium Link, 1809
- Genus Botrypes Preuss, 1852 accepted as Ciliciopodium Corda in J. Sturm, 1831
- Genus Calonectria De Notaris, 1867
- Genus Calostilbe P.A. Saccardo & P. Sydow, 1902
- Genus Calostilbella F. von Höhnel, 1919
- Genus Campylocarpon F. Halleen, H-J. Schroers & P.W. Crous in F. Halleen et al., 2004
- Genus Candelospora Rea & Hawley, 1912 accepted as Calonectria De Notaris, 1867
- Genus Cephalodiplosporium Kamyschko, 1961
- Genus Chaetodochium F. von Höhnel, 1932 accepted as Volutella E.M. Fries, 1832
- Genus Chaetopsina A. Rambelli, 1956
- Genus Chaetopsinectria J. Luo & W.Y. Zhuang, 2010
- Genus Chilonectria P.A. Saccardo, 1878 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Chitinonectria M. Morelet, 1968 accepted as Neonectria Wollenweber, 1917
- Genus Chrysogluten Briosi & Farneti, 1904 accepted as Cosmospora Rabenhorst, 1862
- Genus Ciliciopodium Corda in J. Sturm, 1831
- Genus Ciliciopus F.E. Clements & Shear, 1931 accepted as Ciliciopodium Corda in J. Sturm, 1831
- Genus Coleomyces Moreau & M. Moreau, 1937 accepted as Cylindrocarpon H.W. Wollenweber, 1913
- Genus Corallomyces M.J. Berkeley & M.A. Curtis, 1853 accepted as Corallomycetella Hennings, 1904
- Genus Corallomycetella Hennings, 1904
- Genus Corallonectria C. Herrera & P. Chaverri in Herrera, Rossman, Samuels, Lechat & Chaverri, 2013
- Genus Cosmospora Rabenhorst, 1862
- Genus Creonectria Seaver, 1909 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Curvicladiella Decock & Crous, 2006
- Genus Curvicladium C. Decock & P.W. Crous, 1998
- Genus Cyanochyta F. von Höhnel, 1915
- Genus Cyanonectria G.J. Samuels & P. Chaverri, 2009
- Genus Cyanophomella F. von Höhnel, 1918
- Genus Cylindrium Bonorden, 1851 accepted as Cylindrocarpon H.W. Wollenweber, 1913
- Genus Cylindrocarpon H.W. Wollenweber, 1913
- Genus Cylindrocladiella H.J. Boesewinkel, 1982
- Genus Cylindrocladiopsis J.M. Yen, 1979
- Genus Cylindrocladium A.P. Morgan, 1892 accepted as Calonectria De Notaris, 1867
- Genus Cylindrodendrum Bonorden, 1851
- Genus Dacryoma G.J. Samuels, 1988
- Genus Dematiocladium N. Allegrucci, A.M. Arambarri, M.C. Cazau & P.W. Crous, 2005
- Genus Dialonectria (P.A. Saccardo) M.C. Cooke, 1884 accepted as Cosmospora Rabenhorst, 1862
- Genus Discofusarium Petch, 1921 accepted as Fusarium Link, 1809
- Genus Disco-fusarium T. Petch, 1921 accepted as Fusarium Link, 1809
- Genus Eolichen H. Zukal, 1884 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Eolichenomyces Ciferri & Tomaselli, 1954 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Ephedrosphaera Dumortier, 1822 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Euricoa Batista & H. Maia, 1955 accepted as Cylindrocarpon H.W. Wollenweber, 1913
- Genus Falcocladium S.F. Silveira, A.C. Alfenas, P.W. Crous & M.J. Winglfied in P.W. Crous et al., 1994
- Genus Flagellospora Ingold, 1942
- Genus Fusarium Link, 1809
- Genus Fusidium Link, 1809
- Genus Fusidomus W.B. Grove, 1929 accepted as Fusarium Link, 1809
- Genus Fusisporium Link, 1809 accepted as Fusarium Link, 1809
- Genus Geejayessia H.J. Schroers, T. Gräfenhan & K.A. Seifert, 2011
- Genus Gibberella P.A. Saccardo, 1877
- Genus Gliocephalotrichum J.J. Ellis & C.W. Hesseltine, 1962
- Genus Gliocladiopsis S.B. Saksena, 1954 accepted as Calonectria De Notaris, 1867
- Genus Glionectria P.W. Crous & C.L. Schoch in C.L. Schoch et al., 2000
- Genus Haematonectria Samuels & Nirenberg, 1999
- Genus Hartiella Massee, 1910 accepted as Calostilbella F. von Höhnel, 1919
- Genus Heliscus P.A. Saccardo, 1880
- Genus Hyaloflorea Batista & H. Maia, 1955 accepted as Cylindrocarpon H.W. Wollenweber, 1913
- Genus Knyaria O. Kuntze, 1891 accepted as Tubercularia Tode, 1790
- Genus Lachnidium Giard, 1891 accepted as Fusarium Link, 1809
- Genus Lanatonectria Samuels & Rossman, 1999
- Genus Leuconectria A.Y. Rossman, G.J. Samuels & R. Lowen, 1993
- Genus Lisea P.A. Saccardo, 1877 accepted as Gibberella P.A. Saccardo, 1877
- Genus Lisiella (M.C. Cooke & Massee) P.A. Saccardo, 1891 accepted as Gibberella P.A. Saccardo, 1877
- Genus Longinectria O. Savary, M. Coton, E. Coton & J-L. Jany, 2021
- Genus Macroconia (H.W. Wollenweber) T. Gräfenhan, K.A. Seifert & H.J. Schroers, 2011
- Genus Mariannaea G. Arnaud ex R.A. Samson, 1974
- Genus Megalonectria Spegazzini, 1881 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Microcera Desmazières, 1848 accepted as Fusarium Link, 1809
- Genus Moeszia Bubák, 1914 accepted as Cylindrocarpon H.W. Wollenweber, 1913
- Genus Nalanthamala C.V. Subramanian, 1956
- Genus Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Nectricladiella P.W. Crous & C.L. Schoch in C.L. Schoch et al., 2000
- Genus Nectriella P.A. Saccardo, 1877 accepted as Pseudonectria Seaver, 1909
- Genus Neocosmospora E.F. Smith, 1899
- Genus Neonectria Wollenweber, 1917
- Genus Notarisiella (P.A. Saccardo) F.E. Clements & C.L. Shear, 1931 accepted as Pseudonectria Seaver, 1909
- Genus Ochraceospora M. Fiore, 1930 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Ollula Léveillé, 1863 accepted as Tubercularia Tode, 1790
- Genus Ophionectria P.A. Saccardo, 1878
- Genus Penicillifer J.H. Van Emden, 1968
- Genus Peziotrichum (P.A. Saccardo) J. Lindau in Engler & Prantl, 1900
- Genus Phaeonectria (P.A. Saccardo) P.A. Saccardo & Trotter in P.A. Saccardo, 1913 accepted as Calostilbe P.A. Saccardo & P. Sydow, 1902
- Genus Pionnotes E.M. Fries, 1849 accepted as Fusarium Link, 1809
- Genus Pleogibberella P.A. Saccardo ex Berlese & Voglino in P.A. Saccardo, 1886
- Genus Pleonectria P.A. Saccardo, 1876 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Pleurocolla Petrak, 1924
- Genus Pseudocosmospora C. Herrera & P. Chaverri in Herrera, Rossman, Samuels & Chaverri, 2013
- Genus Pseudofusarium Matsushima, 1971 accepted as Fusarium Link, 1809
- Genus Pseudoidriella P.W. Crous & R.G. Shivas, 2011
- Genus Pseudomicrocera Petch, 1921 accepted as Fusarium Link, 1809
- Genus Pseudonectria Seaver, 1909
- Genus Psilonia E.M. Fries, 1825 accepted as Volutella E.M. Fries, 1832
- Genus Pycnofusarium E. Punithalingam in D. Hawksworth & E. Punithalingam, 1973 accepted as Fusarium Link, 1809
- Genus Rachisia Lindner, 1913 accepted as Fusarium Link, 1809
- Genus Rhodothrix Vainio, 1921 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Rodentomyces F. Doveri, S. Pecchia, S. Sarrocco & G. Vannacci, 2010 accepted as Rodentomyces F. Doveri, S. Pecchia, S. Sarrocco & G. Vannacci in Doveri, 2016
- Genus Rodentomyces F. Doveri, S. Pecchia, S. Sarrocco & G. Vannacci in Doveri, 2016
- Genus Rubrinectria Rossman & Samuels, 1999
- Genus Scoleconectria Seaver, 1909 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Selenosporium Corda, 1837 accepted as Fusarium Link, 1809
- Genus Septofusidium W. Gams, 1971
- Genus Septorella Allescher, 1897 accepted as Fusarium Link, 1809
- Genus Sphaerostilbe L.R. Tulasne & C. Tulasne, 1861 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Sporotrichella P.A. Karsten, 1887 accepted as Fusarium Link, 1809
- Genus Stagonostroma Diedicke, 1914 accepted as Fusarium Link, 1809
- Genus Stalagmites Theissen & H. Sydow, 1914
- Genus Stilbonectria P.A. Karsten, 1889 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Stromateria Corda, 1837 accepted as Tubercularia Tode, 1790
- Genus Styloletendraea Weese, 1924 accepted as Nectria (E.M. Fries) E.M. Fries, 1849
- Genus Stylonectria F. von Höhnel, 1915 accepted as Cosmospora Rabenhorst, 1862
- Genus Tetracytum R. Vanderwalle, 1945 accepted as Calonectria De Notaris, 1867
- Genus Thysanopyxis Rabenhorst ex H.F. Bonorden, 1864 accepted as Volutella E.M. Fries, 1832
- Genus Ticonectria Döbbeler, 1998
- Species Ticonectria perianthii Döbbeler, 1998
- Genus Trichofusarium F. Bubák, 1906 accepted as Fusarium Link, 1809
- Genus Tubecularia accepted as Tubercularia Tode, 1790
- Genus Tubercolarites L. Barsanti, 1903 †
- Genus Tubercularia Tode, 1790
- Genus Ustilaginoidella Essed, 1911 accepted as Fusarium Link, 1809
- Genus Velutella E.M. Fries, 1832 accepted as Volutella E.M. Fries, 1832
- Genus Vermicularia E.M. Fries, 1825
- Genus Viridispora Samuels & Rossman, 1999
- Genus Volutella E.M. Fries, 1832
- Genus Volutellonectria J. Luo & W.-Y. Zhuang, 2012
- Genus Volutina Penzig & P.A. Saccardo, 1901
- Genus Xenocalonectria P.W. Crous & C.L. Schoch in C.L. Schoch et al., 2000
- Genus Xenocylindrocladium C. Decock, G.L. Hennebert & P.W. Crous, 1997
- Genus Xenonectriella Weese, 1919
- Genus Xenostilbum F. Petrak, 1959 accepted as Calostilbella F. von Höhnel, 1919
- Genus Zythiostroma F. von Höhnel ex Falck, 1923
- 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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