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
- Order Abrothallales
- Order Acrospermales
- Order Arthrocatenales
- Order Asterinales
- Order Bezerromycetales accepted as Tubeufiales
- Order Botryosphaeriales
- Order Capnodiales
- Order Catinellales
- Order Cladoriellales
- Order Collemopsidiales
- Order Coniosporiales
- Order Dothideales
- Order Dothideomycetes incertae sedis
- Family Alinaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Aspidotheliaceae
- Family Atichiaceae accepted as Seuratiaceae
- Family Aulographaceae Luttrell ex P.M. Kirk et al., 2001
- Family Balladynaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Brefeldiellaceae accepted as Trichopeltinaceae A.C. Batista, A.A. Costa & R. Ciferri, 1958
- Family Cleistosphaeraceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Coccoideaceae P. Hennings ex Saccardo & D. Saccardo, 1905
- Family Cookellaceae F.X.R. von Höhnel ex Saccardo & Trotter, 1885
- Family Diporothecaceae
- Family Dothideomycetes incertae sedis
- Genus Acerbia (P.A. Saccardo) P.A. Saccardo & P. Sydow, 1899 accepted as Rosenscheldia Spegazzini, 1885
- Genus Achorella Theissen & H. Sydow, 1915
- Genus Acremoniula G. Arnaud, 1954
- Genus Alascospora H.A. Raja, H.A. Violi & C.A. Shearer, 2010
- Genus Anthracostroma Petrak, 1954
- Genus Apiosporella Spegazzini, 1912 accepted as Asteromella Passerini & Thümen, 1880
- Genus Aplosporidium Spegazzini, 1912 accepted as Asteromella Passerini & Thümen, 1880
- Genus Aquamarina J. Kohlmeyer, B. Volkmann-Kohlmeyer & O.E. Eriksson, 1996
- Genus Arthopyreniella J. Steiner in A. Zahlbruckner, 1911 accepted as Mycoglaena F. von Höhnel, 1909
- Genus Ascohansfordiellopsis D. Hawksworth, 1979 accepted as Koordersiella F. von Höhnel, 1909
- Genus Ascominuta V.M. Ranghoo & K.D. Hyde, 2000
- Genus Ascomycetella Saccardo, 1886 accepted as Myriangiopsis P. Hennings, 1902
- Genus Ascostratum H. Sydow & P. Sydow, 1912
- Genus Asteromella Passerini & Thümen, 1880
- Genus Austropleospora R.G. Shivas & L. Morin, 2010
- Genus Bactrodesmium Cooke, 1883
- Genus Bahusakala C.V. Subramanian, 1958
- Genus Belizeana J. Kohlmeyer & B. Volkmann-Kohlmeyer, 1987
- Genus Bertossia Ciferri & Tomaselli, 1953 accepted as Mycoglaena F. von Höhnel, 1909
- Genus Blastophoma Klebahn, 1933 accepted as Sclerophoma F. von Höhnel, 1909
- Genus Bleximothyrium L. Le Renard, R.A. Stockey, G.R. Upchurch & M.L. Berbee, 2021 †
- Genus Botryohypoxylon G.J. Samuels & J.D. Rogers, 1986
- Genus Brachyconidiella R.F. Castañeda Ruiz & W.B. Kendrick, 1990
- Genus Brooksia Hansford, 1956
- Genus Bryopelta P. Döbbeler & J. Poelt in P. Döbbeler, 1978
- Genus Bryorella P. Döbbeler, 1978
- Genus Bryosphaeria P. Döbbeler, 1978
- Genus Bryostroma P. Döbbeler, 1978
- Genus Bryothele Döbbeler, 1998
- Genus Calyptra Theissen & H. Sydow, 1918
- Genus Camarosporula Petrak, 1954
- Genus Capillataspora K.D. Hyde, 1989
- Genus Capnogonium Batista & Peres, 1961 accepted as Brooksia Hansford, 1956
- Genus Catulus D.W. Malloch & C.T. Rogerson, 1978
- Genus Cenococcum Mougeot & E.M. Fries, 1825
- Genus Ceratocarpia L. Rolland, 1896
- Genus Ceratonema Persoon, 1822
- Genus Cercidospora Körber, 1865
- Genus Cerodothis B.N. Muthappa, 1969
- Genus Chaetobotrys F.E. Clements in F.E. Clements & Shear, 1931 accepted as Kusanobotrys P.C. Hennings, 1904
- Genus Chaetomelanops Petrak, 1948 accepted as Pyrenostigme H. Sydow, 1926
- Genus Chaetonectrioides T. Matsushima, 1996
- Genus Chermomyces Brain, 1923
- Genus Ciferriomyces Petrak, 1932 accepted as Pyrenostigme H. Sydow, 1926
- Genus Clypeostroma Theissen & H. Sydow, 1914
- Genus Coniothyriopsiella Bender, 1932 accepted as Cyclothyrium Petrak, 1923
- Genus Coniothyriopsis Petrak, 1923 accepted as Cyclothyrium Petrak, 1923
- Genus Crauatamyces Viégas, 1944
- Genus Cryomyces Selbmann, de Hoog, Mazzaglia, Friedmann & Onofri, 2005
- Genus Cyclothyrium Petrak, 1923
- Genus Cyrtidium Vainio, 1921
- Genus Cyrtidula Minks, 1876
- Genus Cyrtopsis Vainio, 1921
- Genus Cystodium Fée, 1837
- Genus Daruvedia R.W.G. Dennis, 1988
- Genus Dawsophila P. Döbbeler, 1981
- Genus Dendryphiopsis S.J. Hughes, 1953
- Genus Dermatodothis Raciborski ex Theissen & H. Sydow, 1914
- Genus Dexteria F.L. Stevens, 1917 accepted as Hyalosphaera F.L. Stevens, 1917
- Genus Didymocyrtidium Vainio, 1921
- Genus Didymocyrtis Vainio, 1921
- Genus Didymopleella Munk, 1953
- Genus Diederichia D.L. Hawksworth, 2003
- Genus Dilophia P.A. Saccardo, 1883 accepted as Lidophia J. Walker & B.C. Sutton, 1974
- Genus Dilophospora Desmazières, 1840
- Genus Diplochorina Gutner, 1933
- Genus Dipyrgis Clements, 1909
- Genus Discothecium Zopf, 1897 accepted as Endococcus Nylander, 1855
- Genus Disculina F. von Höhnel, 1916
- Genus Dolabra C. Booth & W.P. Ting, 1964
- Genus Elaeomyces Kirchner, 1888
- Genus Elmerinula H. Sydow, 1934
- Genus Enduria Norman, 1885
- Genus Epibotrys Theissen & H. Sydow, 1915 accepted as Gilletiella P.A. Saccardo & P. Sydow, 1899
- Genus Exosporina Oudemans, 1904
- Genus Frondisphaeria K.D. Hyde, 1996
- Genus Geomyces Traaen, 1914
- Genus Gibberidea Fuckel, 1870
- Genus Gibberinula O. Kuntze, 1898 accepted as Gibberidea Fuckel, 1870
- Genus Gilletiella P.A. Saccardo & P. Sydow, 1899
- Genus Glenosporella Nannizzi, 1931 accepted as Geomyces Traaen, 1914
- Genus Globoa A.C. Batista & H.S. Maia in A.C. Batista & R. Ciferri, 1962
- Genus Globulina Spegazzini, 1888
- Genus Gloeodiscus R.W.G. Dennis, 1961
- Genus Grandigallia M.E. Barr, R.T. Hanlin, L. Cedeño, J. Parra & R. Hernandez, 1987
- Genus Grauatamyces Viégas, 1944
- Genus Griggsia F.L. Stevens & Dalbey, 1919
- Genus Hansfordiellopsis F.C. Deighton, 1960
- Genus Harknessiella P.A. Saccardo, 1889
- Genus Harmandiana Bouly de Lesdain, 1914
- Genus Hassea A. Zahlbruckner, 1902
- Genus Hendersoniella (P.A. Saccardo) P.A. Saccardo, 1902 accepted as Hendersoniella Tassi, 1900
- Genus Heptameria Rehm & Thümen, 1879
- Genus Heterochlamys Patouillard in Patouillard & de Lagerheim, 1895 accepted as Gilletiella P.A. Saccardo & P. Sydow, 1899
- Genus Heterosphaeriopsis J. Hafellner, 1979
- Genus Hiospira R.T. Moore, 1962
- Genus Homostegia Fuckel, 1870
- Genus Hyalocrea H. Sydow & P. Sydow, 1917
- Genus Hyalosphaera F.L. Stevens, 1917
- Genus Hyalotexis H. Sydow, 1925 accepted as Hyalosphaera F.L. Stevens, 1917
- Genus Hypobryon P. Döbbeler, 1983
- Genus Hysteropeltella Petrak, 1923
- Genus Hysteropsis Rehm in Rabenhorst, 1887
- Genus Iledon Samuels & J.D. Rogers, 1986
- Genus Keisslerellum Werner, 1944 accepted as Mycoporellum J. Müller Arg., 1884
- Genus Kentingia A. Sivanesan & W.H. Hsieh, 1989
- Genus Keratosphaera H.B.P. Upadhyay, 1964 accepted as Koordersiella F. von Höhnel, 1909
- Genus Kirschsteiniella Petrak, 1923 accepted as Cyclothyrium Petrak, 1923
- Genus Koordersiella F. von Höhnel, 1909
- Genus Kullhemia P.A. Karsten, 1878
- Genus Kusanobotrys P.C. Hennings, 1904
- Genus Lanatosphaera M. Matzer, 1996
- Genus Laterotheca A.C. Batista in A.C. Batista & R. Ciferri, 1963 accepted as Acrogenotheca R. Ciferri & A.C. Batista, 1963
- Genus Lazarenkoa Zerova, 1938
- Genus Leptospora Rabenhorst, 1857
- Genus Leucographa Nylander, 1857
- Genus Leveillina Theissen & H. Sydow, 1915
- Genus Licopolia P.A. Saccardo, H. Sydow & P. Sydow, 1900
- Genus Lidophia J. Walker & B.C. Sutton, 1974
- Genus Limboria Acharius, 1815
- Genus Lineolata J. Kohlmeyer & B. Volkmann-Kohlmeyer, 1990
- Genus Lithopythium Bornet & Flahault, 1891
- Genus Lophiosphaerella Hara, 1948
- Genus Lopholeptosphaeria Sousa da Câmara, 1932
- Genus Macmillanina O. Kuntze, 1898 accepted as Disculina F. von Höhnel, 1916
- Genus Marisolaris J. Koch & E.B.G. Jones, 1989
- Genus Massariola Füisting, 1868
- Genus Megaloseptoria Naumov, 1925
- Genus Melanobotrys L. Rodway, 1926 accepted as Xylobotryum Patouillard, 1895
- Genus Melanochlamys H. Sydow & P. Sydow in O. Fuhrmann & E. Mayor, 1914 accepted as Gilletiella P.A. Saccardo & P. Sydow, 1899
- Genus Microcyclella Theissen, 1914
- Genus Micromastia Spegazzini, 1909
- Genus Minteriella G. Heredia, R.F. Castañeda Ruiz & R.M. Arias in Heredia, Castañeda, Arias, Gamboa-Angulo & De La Rosa, 2012
- Genus Monodictys S. Hughes, 1958
- Genus Montagnella Spegazzini, 1881
- Genus Moriolomyces Ciferri & Tomaselli, 1953
- Genus Mucomassaria Petrak & Ciferri, 1932
- Genus Mycocryptospora J. Reid & C. Booth, 1987
- Genus Mycoglaena F. von Höhnel, 1909
- Genus Mycoporellum J. Müller Arg., 1884
- Genus Mycoporis Clements, 1909
- Genus Mycoporopsis J. Müller Arg., 1885
- Genus Mycothyridium Petrak, 1962
- Genus Myriangiopsis P. Hennings, 1902
- Genus Myriostigma G. Arnaud, 1925 accepted as Myriostigmella G. Arnaud, 1952
- Genus Myriostigmella G. Arnaud, 1952
- Genus Mytilostoma P.A. Karsten, 1880
- Genus Myxophora P. Döbbeler & J. Poelt, 1978
- Genus Naemosphaera (Saccardo) Saccardo, 1892
- Genus Naemostroma F. von Höhnel, 1919 accepted as Septoriella Oudemans, 1889
- Genus Naumovia Dobrozrakova, 1928 accepted as Rosenscheldia Spegazzini, 1885
- Genus Nemacola A. Massalongo, 1855
- Genus Neonorrlinia H. Sydow, 1923 accepted as Cercidospora Körber, 1865
- Genus Neoventuria H. Sydow & P. Sydow, 1919
- Genus Norrlinia Vainio, 1921 accepted as Cercidospora Körber, 1865
- Genus Overeemia Arnaud, 1954 accepted as Brooksia Hansford, 1956
- Genus Parmulariella P.C. Hennings, 1904
- Genus Passeriniella Berlese, 1891
- Genus Peltaster H. Sydow & P. Sydow, 1917
- Genus Peroschaeta Batista & A.F. Vital, 1957
- Genus Phacidiostromella F. von Höhnel, 1917
- Genus Phaeocyrtidula Vainio, 1921
- Genus Phaeoglaena Clements, 1909
- Genus Phaeopeltium F.E. Clements & Shear, 1931 accepted as Phaeopeltosphaeria Berlese & Peglion, 1892
- Genus Phaeopeltosphaeria Berlese & Peglion, 1892
- Genus Phaeophragmocauma F.L. Stevens, 1931 accepted as Dermatodothis Raciborski ex Theissen & H. Sydow, 1914
- Genus Phaeosclera L. Sigler, A. Tsuneda & J.W. Carmichael, 1981
- Genus Phaeosperma Nitschke ex Fuckel, 1870
- Species Phaeosperma anserinum (Pers.) Traverso, 1911 accepted as Valsaria anserina (Pers.) Sacc., 1878
- Species Phaeosperma apiculatum (Curr.) Sacc. & Traverso, 1911 accepted as Apiorhynchostoma curreyi (Rabenh.) E. Müll., 1962
- Species Phaeosperma foedans P. Karst., 1873 accepted as Pseudovalsaria ferruginea (Nitschke) Rappaz, 1995
- Species Phaeosperma gastrinum (Fr.) Nitschke accepted as Anthostoma gastrinum (Fr.) Sacc., 1873
- Species Phaeosperma niesslii G. Winter accepted as Pseudovalsaria ferruginea (Nitschke) Rappaz, 1995
- Genus Phaeothecoidiella J.C. Batzer & P.W. Crous, 2010
- Genus Phaeotomasellia K. Katumoto, 1981
- Genus Phanerococculus Ciferri, 1954
- Genus Phanerococcus Theissen & H. Sydow, 1918 accepted as Koordersiella F. von Höhnel, 1909
- Genus Phelonites Fries, 1846
- Genus Phelonitis F.F. Chevallier, 1826
- Genus Philobryon P. Döbbeler, 1988
- Genus Philonectria K. Hara, 1914
- Genus Phragmodimerium Petrak & Ciferri, 1932 accepted as Philonectria K. Hara, 1914
- Genus Phragmoscutella Woronichin & Abramov, 1926
- Genus Phycorella P. Döbbeler, 1980
- Genus Physalosporopsis Batista & H. Maia, 1955
- Genus Plagiostromella F. von Höhnel, 1917
- Genus Plectophoma F. von Höhnel, 1907 accepted as Asteromella Passerini & Thümen, 1880
- Genus Pleosphaerellula Naumov & Czerepanova, 1952
- Genus Pleosphaeropsis E.A. Vainio, 1921 accepted as Cercidospora Körber, 1865
- Genus Pleotrichiella A. Sivanesan, 1984
- Genus Pleurostromella Petrak, 1922
- Genus Poeltia Petrak, 1972 accepted as Hyalocrea H. Sydow & P. Sydow, 1917
- Genus Poeltiella Petrak, 1974 accepted as Hyalocrea H. Sydow & P. Sydow, 1917
- Genus Polysporidiella F. Petrak, 1960
- Genus Polystomellopsis F. Stevens, 1924
- Genus Porterula Spegazzini, 1920 accepted as Asteromella Passerini & Thümen, 1880
- Genus Potamomyces K.D. Hyde, 1995
- Genus Prolisea Clements in Clements & Shear, 1931 accepted as Cercidospora Körber, 1865
- Genus Pseudoendococcus Marchand, 1896 accepted as Endococcus Nylander, 1855
- Genus Pseudomorfea E. Punithalingam, 1981
- Genus Pseudopleospora Petrak, 1920
- Genus Pseudoramichloridium R. Cheewangkoon & P.W. Crous, 2009
- Genus Pteridiospora Penzig & P.A. Saccardo, 1897
- Genus Pteromycula P.F. Cannon, 1997
- Genus Punctillum Petrak & H. Sydow, 1924
- Genus Pyrenochium Link, 1833
- Genus Pyrenocyclus Petrak, 1955
- Genus Pyrenostigme H. Sydow, 1926
- Genus Rachidicola K.D. Hyde & J. Fröhlich in K.D. Hyde, 1995
- Genus Racovitziella P. Döbbeler & J. Poelt in P. Döbbeler, 1978
- Genus Rehmiomycella E. Müller in E. Müller & J.A. von Arx, 1962
- Genus Rehmiomyces (P.A. Saccardo & P. Sydow) H. Sydow, 1904 accepted as Rehmiomycella E. Müller in E. Müller & J.A. von Arx, 1962
- Genus Repetophragma C.V. Subramanian, 1992
- Genus Rhizopycnis D.F. Farr, 1998
- Genus Rosasphaeria W.M. Jaklitsch & H. Voglmayr, 2012
- Genus Rosellinula R. Santesson in O. Eriksson & D.L. Hawksworth, 1986
- Genus Rosenscheldia Spegazzini, 1885
- Genus Rosenschoeldia L. Holm, 1968 accepted as Rosenscheldia Spegazzini, 1885
- Genus Rostafinsckia Spegazzini, 1880
- Genus Rostafinskia Spegazzini, 1880
- Genus Roumegueria (P.A. Saccardo) P.C. Hennings, 1908
- Genus Roussoellopsis I. Hino & K. Katumoto, 1965
- Genus Roussoëllopsis I. Hino & Katumoto, 1965 represented as Roussoellopsis I. Hino & K. Katumoto, 1965
- Genus Salsuginea K.D. Hyde, 1991
- Genus Sampaioa González Fragoso, 1923 accepted as Mycoglaena F. von Höhnel, 1909
- Genus Santiella Tassi, 1900 accepted as Passeriniella Berlese, 1891
- Genus Saxomyces L. Selbmann & D. Isola in Wijayawardene et al., 2017
- Genus Saxomyces L. Selbmann & D. Isola in Selbmann, Isola, Egidi, Zucconi, Gueidan, de Hoog & Onofri, 2013 accepted as Saxomyces L. Selbmann & D. Isola in Wijayawardene et al., 2017
- Genus Schizophoma Klebahn, 1933 accepted as Sclerophoma F. von Höhnel, 1909
- Genus Scleroconidioma A. Tsuneda, R.S. Currah & Thormann in A. Tsuneda et al., 2000
- Genus Sclerophoma F. von Höhnel, 1909
- Genus Scolecobonaria A.C. Batista in A.C. Batista & R. Ciferri, 1962
- Genus Semifissispora H.J. Swart, 1982
- Genus Semisphaeria K. Holm & L. Holm, 1991
- Genus Septonema Corda, 1837
- Genus Septoriella Oudemans, 1889
- Genus Sorothelia Körber, 1865 accepted as Endococcus Nylander, 1855
- Genus Stichophoma Klebahn, 1933 accepted as Sclerophoma F. von Höhnel, 1909
- Genus Stictochorella F. von Höhnel, 1917 accepted as Asteromella Passerini & Thümen, 1880
- Genus Stictochorellina Petrak, 1922 accepted as Asteromella Passerini & Thümen, 1880
- Genus Stigmatea Fries, 1849
- Genus Stigmea E.M. Fries, 1836
- Genus Stomatothyrium L. Le Renard, R.A. Stockey, G.R. Upchurch & M.L. Berbee, 2021 †
- Genus Stuartella Fabre, 1879
- Genus Tamsiniella S.-W. Wong, K.D. Hyde, W.-H. Ho & S.J. Stanley, 1998
- Genus Teichosporella (P.A. Saccardo) P.A. Saccardo, 1895
- Genus Teratoschaeta A.C. Batista & O.M. Fonseca, 1967
- Genus Thalassoascus Ollivier, 1926
- Genus Thelenidia Nylander, 1886
- Genus Thelenidiomyces Ciferri & Tomaselli, 1953 accepted as Thelenidia Nylander, 1886
- Genus Thryptospora Petrak, 1947
- Genus Tilakiella B.V. Srinivasula, 1973
- Genus Tomeoa I. Hino, 1954
- Genus Trachyxylaria A. Møller, 1901 accepted as Xylobotryum Patouillard, 1895
- Genus Trematosphaeriopsis Elenkin, 1901 accepted as Homostegia Fuckel, 1870
- Genus Trematosphaeris Clements & Shear, 1931 accepted as Homostegia Fuckel, 1870
- Genus Trichoplacia A. Massalongo, 1853
- Genus Trichospora
- Genus Vainiona R.G. Werner, 1943 accepted as Cercidospora Körber, 1865
- Genus Venturiella Spegazzini, 1909 accepted as Neoventuria H. Sydow & P. Sydow, 1919
- Genus Verlotia Fabre, 1879 accepted as Heptameria Rehm & Thümen, 1879
- Genus Wernerella P. Navarro-Rosinés, C. Roux & M. Giralt, 1998
- Genus Westea H.J. Swart, 1988
- Genus Xylobotryum Patouillard, 1895
- Genus Xyloceras A.L. Smith, 1901 accepted as Xylobotryum Patouillard, 1895
- Genus Xylocreas A.L. Smith, 1901 accepted as Xylobotryum Patouillard, 1895
- Genus Xylosphaeria G.H. Otth, 1869 accepted as Mycothyridium Petrak, 1962
- Genus Zignoina M.C. Cooke, 1885
- Family Dubujianaceae D. Pem, M. Doilom & K.D. Hyde in Pem et al., 2019
- Family Dysrhynchaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Endosporiaceae D. Pem, M. Doilom & K.D. Hyde in Pem et al., 2019
- Family Englerulaceae P. Hennings, 1904
- Family Eoterfeziaceae
- Family Epigloeaceae
- Family Homortomycetaceae K.M. Thambugala, A.J.L. Phillips & K.D. Hyde, 2016
- Family Hyalomeliolinaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Lautosporaceae
- Family Leptopeltidaceae von Höhnel ex Trotter, 1928
- Family Macrovalsariaceae D. Pem, M. Doilom & K.D. Hyde in Pem et al., 2019
- Family Mastodiaceae
- Family Meliolinaceae S. Hughes, 1993
- Family Mesnieraceae Arx & Müller, 1975
- Family Microglaenaceae accepted as Thelenellaceae
- Family Myxotrichaceae
- Family Naetrocymbaceae R.C. Harris, 1995
- Family Nematotheciaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Neoparodiaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Palawaniaceae A. Mapook & K.D. Hyde in Mapook et al., 2016
- Family Paranectriellaceae S. Boonmee & K.D. Hyde in Hyde et al., 2013
- Family Parodiellaceae Theissen & Sydow ex M.E. Barr, 1987
- Family Peltasteraceae accepted as Dothideomycetes incertae sedis
- Family Perisporiopsidaceae E. Müller & J.A. von Arx ex R. Kirschner & T.A. Hofmann, 2012
- Family Phaeodimeriellaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Phaneromycetaceae
- Family Pododimeriaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Polyclypeolinaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Protoscyphaceae Kutorga & D. Hawksworth, 1997
- Family Protothelenellaceae
- Family Pseudeurotiaceae
- Family Pseudoperisporiaceae Toro, in Seaver & Palacios Chardon, 1926
- Family Pseudorobillardaceae P.W. Crous in Crous et al., 2019
- Family Pyrenidiaceae A. Zahlbruckner in Engler, 1898
- Family Pyrenothricaceae
- Family Pyrenotrichaceae accepted as Pyrenothricaceae
- Family Roesleriaceae
- Family Seuratiaceae
- Family Seynesiopeltidaceae K.D. Hyde in Hyde et al., 2013
- Family Stomatogenaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Stomatogeneceae accepted as Stomatogenaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Thelenellaceae
- Family Thrombiaceae
- Family Thyrinulaceae X.Y. Zeng, S. Hongsanan & K.D. Hyde, 2020
- Family Toroaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2017
- Family Trichopeltinaceae A.C. Batista, A.A. Costa & R. Ciferri, 1958
- Family Trichothyriaceae Theissen, 1914
- Order Dothideomycetidae incertae sedis
- Order Dyfrolomycetales
- Order Eremithallales
- Order Eremomycetales
- Order Hysteriales
- Order Jahnulales
- Order Kirschsteiniotheliales
- Order Koralionastetales
- Order Lembosinales
- Order Lichenotheliales
- Order Meliolales
- Order Microthyriales
- Order Minutisphaerales
- Order Monoblastiales
- Order Murramarangomycetales
- Order Muyocopronales
- Order Myriangiales
- Order Mytilinidiales
- Order Natipusillales
- Order Neodactylariales
- Order Parmulariales
- Order Patellariales
- Order Phaeotrichales
- Order Pleosporales
- Order Stigmatodiscales
- Order Strigulales
- Order Superstratomycetales
- Order Trypetheliales
- Order Tubeufiales
- Order Valsariales
- Order Venturiales
- Order Wiesneriomycetales accepted as Tubeufiales
- Order Zeloasperisporiales
- 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
- 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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