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 Pisorisporiales
- 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
- 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
- Genus Acanthodochium G.J. Samuels, J.D. Rogers & E. Nagasawa, 1987
- Genus Acrosphaeria Corda, 1842 accepted as Xylaria Hill ex Schrank, 1789
- Genus Acrostaphylus G. Arnaud ex Subramanian, 1956 accepted as Nodulisporium Preuss in Rabenhorst, 1849
- Genus Albocrustum Lloyd, 1925 accepted as Biscogniauxia O. Kuntze, 1891
- Genus Alocospora J.C. Krug, 1990
- Genus Amphirosellinia Y.M. Ju, J.D. Rogers, H.M. Hsieh & L. Vasilyeva, 2005
- Genus Annellosporium M.L. Davey, 2010
- Genus Annulohypoxylon Y.M. Ju, J.D. Rogers & H.M. Hsieh, 2005
- Genus Anthostomella P.A. Saccardo, 1875
- Genus Appendixia B.S. Lu & K.D. Hyde, 2000
- Genus Areolospora S.C. Jong & E.E. Davis, 1974
- Genus Arthroxylaria K.A. Seifert & W. Gams, 2002
- Genus Ascostroma Bonorden, 1851 accepted as Kretzschmaria E.M. Fries, 1849
- Genus Ascotricha Berkeley, 1838
- Genus Ascovirgaria J.D. Rogers & Y.M. Ju, 2002
- Genus Astrocystis Berkeley & Broome, 1873
- Genus Bacillaria Montagne, 1840 accepted as Camillea E.M. Fries, 1849
- Genus Barrmaelia F. Rappaz, 1995
- Genus Basidiobotrys F. von Höhnel, 1909 accepted as Xylocladium Sydow ex Lindau in Engler & Prantl, 1900
- Genus Biscogniauxia O. Kuntze, 1891
- Genus Byssitheca Bonorden, 1864 accepted as Rosellinia de Notaris, 1844
- Genus Calceomyces S.-I. Udagawa & S. Ueda, 1988
- Genus Camillea E.M. Fries, 1849
- Genus Cannonia J.E. Taylor & K.D. Hyde, 1999
- Genus Carnostroma C.G. Lloyd, 1919 accepted as Xylaria Hill ex Schrank, 1789
- Genus Ceratocladium Patouillard, 1898 accepted as Xylocladium Sydow ex Lindau in Engler & Prantl, 1900
- Genus Cerillum Clements in Clements & Shear, 1931 accepted as Engleromyces Hennings, 1900
- Genus Chaenocarpus Rebentisch, 1804
- Genus Chaenocarpus Léveillé, 1843 accepted as Chaenocarpus Rebentisch, 1804
- Genus Chaenocarpus K.P.J. Sprengel, 1831 accepted as Chaenocarpus Rebentisch, 1804
- Genus Chlorostroma A.N. Miller, Lar.N. Vassiljeva & J.D. Rogers, 2007
- Genus Chromocreopsis Seaver, 1910 accepted as Thuemenella Penzig & Saccardo, 1898
- Genus Coelorhopalon Overeem in Overeem & Weese, 1925(?) accepted as Xylaria Hill ex Schrank, 1789
- Genus Coenocarpus E.M. Fries, 1825 accepted as Chaenocarpus Rebentisch, 1804
- Genus Colletomanginia Hariot & Patouillard, 1906 accepted as Engleromyces Hennings, 1900
- Genus Collodiscula I. Hino & Katumoto, 1955
- Genus Coniolaria Seigle-Murandi, Guiraud, Steiman & Sage, 1995
- Genus Coniolariella D. García, Stchigel & Guarro, 2006
- Genus Coprolepa Fuckel, 1870 accepted as Hypocopra (E.M. Fries) J. Kickx f., 1867
- Genus Creosphaeria Theissen, 1910
- Genus Cryptosordaria De Notaris ex Saccardo, 1891 accepted as Anthostomella P.A. Saccardo, 1875
- Genus Cryptothamnium Wallroth, 1842 accepted as Chaenocarpus Rebentisch, 1804
- Genus Cyanopulvis J. Fröhlich & K.D. Hyde, 2000
- Genus Daldinia Cesati & De Notaris, 1863
- Genus Dematophora R. Hartig, 1883
- Genus Diamantinia A.N. Miller, Laessøe & Huhndorf, 2003
- Genus Diatrypeopsis Spegazzini, 1884 accepted as Camillea E.M. Fries, 1849
- Genus Dicyma E. Boulanger, 1897
- Genus Discosphaera Dumortier, 1822 accepted as Hypoxylon Bulliard, 1791
- Genus Discoxylaria J.C. Lindquist & J.E. Wright, 1964
- Genus Durotheca T. Læssøe, P. Srikitikulchai, J.J.D. Luangsa-ard & M. Stadler, 2013
- Genus Emarcea L.M. Duong, R. Jeewon & K.D. Hyde in L.M. Duong et al., 2004
- Genus Engleromyces Hennings, 1900
- Genus Entoleuca H. Sydow, 1922
- Genus Entonaema A. Møller, 1901
- Genus Entosordaria Spegazzini, 1920 accepted as Anthostomella P.A. Saccardo, 1875
- Genus Epixylon Füisting, 1867 accepted as Hypoxylon Bulliard, 1791
- Genus Euepixylon Füisting, 1867
- Genus Euhypoxylon Füisting, 1867 accepted as Hypoxylon Bulliard, 1791
- Genus Fuckelia (Nitschke ex Saccardo) Cooke, 1869 accepted as Euepixylon Füisting, 1867
- Genus Gamosphaera Dumortier, 1822 accepted as Nemania Gray, 1821
- Genus Geniculisporium accepted as Nemania Gray, 1821
- Genus Geniculisynnema Okane & Nakagiri, 2007
- Genus Geniculosporium C.G.C. Chesters & G.N. Greenhalgh, 1964 accepted as Nemania Gray, 1821
- Genus Gigantospora B.S. Lu & K.D. Hyde, 2003
- Genus Gonytrichella Emoto & Tubaki, 1971
- Genus Guestia G.J.D. Smith & K.D. Hyde, 2001
- Genus Halorosellinia A.J.S. Whalley, E.B.G. Jones, K.D. Hyde & T. Laessøe, 2000
- Genus Helicogermslita B.C. Lodha & D.L. Hawksworth in D.L. Hawksworth & B.C. Lodha, 1983
- Genus Hemisphaeria Klotzsch, 1843 accepted as Daldinia Cesati & De Notaris, 1863
- Genus Henningsina A. Møller, 1901 accepted as Phylacia J.H. Léveillé, 1845
- Genus Holttumia Lloyd, 1924
- Species Holttumia congregata Lloyd, 1924 accepted as Kretzschmaria macrosperma (Mont.) J.D. Rogers & Y.M. Ju, 1998
- Genus Hypocopra (E.M. Fries) J. Kickx f., 1867
- Genus Hypocreodendron Hennings, 1897
- Genus Hypoxylina Starbäck, 1905 accepted as Hypoxylon Bulliard, 1791
- Genus Hypoxylon Bulliard, 1791
- Genus Hypoxylon Adanson, 1763 accepted as Xylaria Hill ex Schrank, 1789
- Genus Induratia G.J. Samuels, E. Müller & O. Petrini, 1987
- Genus Institale E.M. Fries, 1829 accepted as Hypoxylon Bulliard, 1791
- Genus Jongiella M. Morelet, 1971 accepted as Camillea E.M. Fries, 1849
- Genus Jumillera J.D. Rogers, Y.M. Ju & F. San Martín, 1997
- Genus Kommamyce Nieuwland, 1916 accepted as Biscogniauxia O. Kuntze, 1891
- Genus Kretzschmaria E.M. Fries, 1849
- Genus Kretzschmariella Viégas, 1944
- Genus Leprieuria T. Laessøe, J.D. Rogers & A.J.S. Whalley, 1989
- Genus Leptomassaria Petrak, 1914 accepted as Anthostomella P.A. Saccardo, 1875
- Genus Leveillea E.M. Fries, 1849 accepted as Phylacia J.H. Léveillé, 1845
- Genus Lichenagaricus P. Micheli, 1729 accepted as Xylaria Hill ex Schrank, 1789
- Genus Lindquistia C.V. Subramanian & K.V. Chandrashekara, 1977
- Genus Lopadostoma (Nitschke) Traverso, 1906
- Genus Maurinia Niessl, 1876 accepted as Anthostomella P.A. Saccardo, 1875
- Genus Moelleroclavus Hennings, 1902 accepted as Xylaria Hill ex Schrank, 1789
- Genus Muscodor Worapong, Strobel & W.M. Hess, 2001
- Genus Myconeesia Kirschstein, 1936
- Genus Neesiella Kirschstein, 1935 accepted as Myconeesia Kirschstein, 1936
- Genus Nemania Gray, 1821
- Genus Neoxylaria S. Konta & K.D. Hyde in Konta et al., 2020
- Genus Nodulisporium Preuss in Rabenhorst, 1849
- Genus Nummularia L.R. Tulasne & C. Tulasne, 1863 accepted as Biscogniauxia O. Kuntze, 1891
- Genus Nummulariella F.-E. Eckblad & A. Granmo, 1978 accepted as Biscogniauxia O. Kuntze, 1891
- Genus Nummularioidea (Cooke & Massee) Lloyd, 1924 accepted as Camillea E.M. Fries, 1849
- Genus Numulariola H.D. House, 1925 accepted as Biscogniauxia O. Kuntze, 1891
- Genus Obolarina Z. Pouzar, 1986
- Genus Occultitheca J.D. Rogers & Y.-M. Ju, 2003
- Genus Ophiorosellinia J.D. Rogers, A. Hidalgo, F.A. Fernández & S.M. Huhndorf, 2004
- Genus Padixonia Subramanian, 1972
- Genus Paramphisphaeria F.A. Fernández, J.D. Rogers, Y.M. Ju, S.M. Huhndorf & L. Umaña, 2004
- Genus Paranthostomella Spegazzini, 1910 accepted as Anthostomella P.A. Saccardo, 1875
- Genus Paucithecium C.G. Lloyd, 1923
- Genus Pedisordaria F.E. Clements, 1909
- Genus Penzigia P.A. Saccardo in P.A. Saccardo & Paoletti, 1888 accepted as Xylaria Hill ex Schrank, 1789
- Genus Peripherostoma S.F. Gray, 1821 accepted as Daldinia Cesati & De Notaris, 1863
- Genus Perisphaeria Roussel, 1806 accepted as Hypoxylon Bulliard, 1791
- Genus Phaeophomatospora Spegazzini, 1909 accepted as Anthostomella P.A. Saccardo, 1875
- Genus Phylacia J.H. Léveillé, 1845
- Genus Pleurographium G. Goidanich, 1935 accepted as Nodulisporium Preuss in Rabenhorst, 1849
- Genus Podosordaria J.B. Ellis & Holway, 1897
- Genus Porodiscella Viégas, 1944 accepted as Xylaria Hill ex Schrank, 1789
- Genus Poroleprieuria M.C. González, R.T. Hanlin, M. Ulloa & E. Aguirre, 2004
- Genus Poronia S.F. Gray, 1821
- Genus Poronia Willdenow, 1787
- Genus Poroniopsis Spegazzini, 1922 accepted as Hypocreodendron Hennings, 1897
- Genus Pseudoxylaria Boedijn, 1959 accepted as Xylaria Hill ex Schrank, 1789
- Genus Puciola M. de Bertoldi, 1976 accepted as Dicyma E. Boulanger, 1897
- Genus Pulveria D.W. Malloch & C.T. Rogerson, 1977
- Genus Pyrenodermium H.F. Bonorden, 1851 accepted as Hypoxylon Bulliard, 1791
- Genus Pyrenomyxa A.P. Morgan, 1895 accepted as Pulveria D.W. Malloch & C.T. Rogerson, 1977
- Genus Pyrenopolyporus C.G. Lloyd, 1917 accepted as Daldinia Cesati & De Notaris, 1863
- Genus Rhopalopsis M.C. Cooke, 1883 accepted as Kretzschmaria E.M. Fries, 1849
- Genus Rhopalostroma D.L. Hawksworth, 1977
- Genus Rosellinia de Notaris, 1844
- Genus Rostrohypoxylon J. Fournier & M. Stadler, 2010
- Genus Sabalicola K.D. Hyde, 1995
- Genus Sarcoxylon M.C. Cooke, 1883
- Genus Sarcoxylum Clements & Shear, 1931 accepted as Sarcoxylon M.C. Cooke, 1883
- Genus Sclerodermatopsis Torrend, 1923 accepted as Xylaria Hill ex Schrank, 1789
- Genus Simoninus Roumeguère, 1879 accepted as Chaenocarpus Rebentisch, 1804
- Genus Spermatodermia Wallroth, 1833 accepted as Hypoxylon Bulliard, 1791
- Genus Spermodermia Tode, 1790 accepted as Hypoxylon Bulliard, 1791
- Genus Sphaeria Haller, 1768
- Genus Spirodecospora B.S. Lu, K.D. Hyde & W.H. Ho, 1998
- Genus Spirogramma Ferdinandsen & Winge, 1909 accepted as Xylaria Hill ex Schrank, 1789
- Genus Squamotubera P.C. Hennings, 1903 accepted as Sarcoxylon M.C. Cooke, 1883
- Genus Stilbohypoxylon P.C. Hennings, 1902
- Genus Streblema Chevallier, 1826
- Genus Striatodecospora D.Q. Zhou, K.D. Hyde & B.S. Lu, 2000
- Genus Stromatoneurospora S.C. Jong & E.E. Davis, 1973
- Genus Stromatosphaeria Greville, 1824 accepted as Daldinia Cesati & De Notaris, 1863
- Genus Stromne F.E. Clements, 1909 accepted as Engleromyces Hennings, 1900
- Genus Thamnomyces C.G. Ehrenberg, 1820
- Genus Theissenia A. Maublanc, 1914
- Genus Thuemenella Penzig & Saccardo, 1898
- Genus Triplicaria P.A. Karsten, 1889
- Genus Ustulina L.R. Tulasne & C. Tulasne, 1863
- Genus Versiomyces A.J.S. Whalley & R. Watling, 1989
- Genus Virgaria C.G.D. Nees, 1816
- Genus Vivantia J.D. Rogers, Y.-M. Ju & Candoussau, 1996
- Genus Vrikshopama D. Rao & P.R. Rao, 1964 accepted as Dematophora R. Hartig, 1883
- Genus Wawelia Namyslowski, 1908
- Genus Whalleya J.D. Rogers, Y.M. Ju & F. San Martín, 1997
- Genus Xylaria Hill ex Schrank, 1789
- Genus Xylariodiscus Hennings, 1899 accepted as Xylaria Hill ex Schrank, 1789
- Genus Xylocladium Sydow ex Lindau in Engler & Prantl, 1900
- Genus Xylocoremium J.D. Rogers, 1984
- Genus Xylocrea A. Møller, 1901 accepted as Sarcoxylon M.C. Cooke, 1883
- Genus Xylosphaera Dumortier, 1822 accepted as Xylaria Hill ex Schrank, 1789
- Genus Xylotumulus J.D. Rogers, Y.M. Ju & Hemmes, 2006
- 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 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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