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
- 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
- Family Ageratinicolaceae L. Lu, K.D. Hyde & S. Tibpromma in Senanayake et al., 2023
- Family Aigialaceae S. Suetrong, J. Sakayaroj, E.B.G. Jones, J. Kohlmeyer, B. Volkmann-Kohlmeyer & C.L. Schoch, 2009
- Family Amniculicolaceae Zhang et al., 2009
- Family Anteagloniaceae K.D. Hyde, J.K. Liu & A. Mapook in Hyde et al., 2013
- Family Arthopyreniaceae W. Watson, 1929
- Family Arthropyreniaceae accepted as Arthopyreniaceae W. Watson, 1929
- Family Astrosphaeriellaceae R. Phookamsak & K.D. Hyde in Liu et al., 2015
- Family Bambusicolaceae D.Q. Dai & K.D. Hyde in Hyde et al., 2013
- Family Biatriosporaceae K.D. Hyde in Hyde et al., 2013
- Family Corynesporascaceae
- Family Cucurbitariaceae
- Family Dacampiaceae
- Family Delitschiaceae
- Family Diademaceae
- Family Dictyosporiaceae S. Boonmee & K.D. Hyde in Boonmee et al., 2016
- Family Didymellaceae J. de Gruyter, M.M. Aveskamp & G.J.M. Verkley, 2009
- Family Didymosphaeriaceae Munk, 1953
- Family Dothidotthiaceae Crous & A.J.L. Phillips, 2008
- Family Fenestellaceae
- Family Halojulellaceae S. Suetrong, K.D. Hyde & E.B.G. Jones in Ariyawansa, Jones, Suetrong, Alias, Kang & Hyde, 2013
- Family Halotthiaceae Y. Zhang, J. Fournier & K.D. Hyde, in Zhang, Fournier, Phookamsak, Bahkali & Hyde, 2013
- Family Lentitheciaceae Zhang et al., 2009
- Family Leptosphaeriaceae
- Family Ligninsphaeriaceae J.F. Zhang, J.K. Liu & Z.Y. Liu, 2016
- Family Lindgomycetaceae K. Hirayama, K. Tanaka & C.A. Shearer in Hirayama et al., 2010
- Family Longiostiolaceae Phukhamsakda, Doilom & K.D. Hyde, 2020
- Family Longipedicellataceae C. Phukhamsada, J. Bhat & K.D. Hyde in Phukhamsakda et al., 2016
- Family Lophiostomataceae
- Family Massarinaceae
- Family Melanommataceae G. Winter, 1885
- Family Montagnulaceae
- Family Morosphaeriaceae Suetrong, Sakayaroj, E.B.G. Jones & C.L. Schoch, 2009
- Family Neohendersoniaceae A. Giraldo & P.W. Crous in Giraldo et al., 2017
- Family Parabambusicolaceae K. Tanaka & K. Hirayama in Tanaka et al., 2015
- Family Paralophiostomataceae V.V. Sarma & M. Niranjan in Hongsanan et al., 2020
- Family Phaeosphaeriaceae M.E. Barr, 1979
- Family Phomaceae accepted as Pleosporales incertae sedis
- Family Pleomassariaceae
- Family Pleomonodictydaceae Hernández-Restrepo, Mena-Portales & Gené, 2017
- Family Pleosporaceae
- Family Pleosporales incertae sedis
- Genus Aigialus J. Kohlmeyer & S. Schatz, 1986
- Genus Amarenographium O.E. Eriksson, 1982
- Genus Amarenomyces O.E. Eriksson, 1981
- Genus Anguillospora Ingold, 1942
- Genus Ansatospora A.G. Newhall, 1944 accepted as Mycocentrospora F.C. Deighton, 1972
- Genus Aquasubmersa K.D. Hyde & H. Zhang in Zhang, Hyde, McKenzie, Bahkali & Zhou, 2012
- Genus Aquaticheirospora Kodsueb & W.H. Ho, 2007
- Genus Aschochytella F. Tassi, 1902
- Genus Ascochyta Libert, 1830
- Genus Ascochytella F. Tassi, 1902 accepted as Ascochyta Libert, 1830
- Genus Ascochytula (Potebnia) Diedicke, 1912 accepted as Ascochyta Libert, 1830
- Genus Ascorhombispora L. Cai & K.D. Hyde, 2007
- Genus Ascoronospora Matsushima, 2003
- Genus Atradidymella M.L. Davey & R.S. Currah, 2009
- Genus Blastostroma C.Z. Wei, Y. Harada & K. Katumoto, 1998
- Genus Botryosporium Schweinitz, 1832 accepted as Dictyosporium Corda, 1836
- Genus Briansuttonia R.F. Castañeda, D.W. Minter & M. Saikawa in Castañeda Ruiz, 2004
- Genus Cattanea Garovaglio, 1875 accepted as Dictyosporium Corda, 1836
- Genus Centrospora Neergaard, 1942 accepted as Mycocentrospora F.C. Deighton, 1972
- Genus Cephalotrichum M.J. Berkeley ex P.A. Saccardo, 1886 accepted as Periconia Tode, 1791
- Genus Cheiromoniliophora S.S. Tzean & J.L. Chen, 1990
- Genus Cheirosporium L. Cai & K.D. Hyde, 2008
- Genus Chlamydosporium Peyronel, 1913 accepted as Phoma P.A. Saccardo, 1880
- Genus Clavariopsis De Wildeman, 1895
- Genus Coronospora M.B. Ellis, 1971
- Genus Cryptodidymosphaerites Currah, Stockey & B.A. LePage, 1998 †
- Genus Dactuliochaeta G.L. Hartman & J.B. Sinclair, 1988
- Genus Dactuliophora C.L.A. Leakey, 1964
- Genus Deuterophoma Petri, 1929 accepted as Phoma P.A. Saccardo, 1880
- Genus Dictyosporium Corda, 1836
- Genus Didymella Saccardo, 1880
- Genus Didymocrea Kowalski, 1965
- Genus Didymotrichia Berlese, 1893 accepted as Neopeckia P.A. Saccardo, 1883
- Genus Digitodesmium P.M. Kirk, 1981
- Genus Dothidotthia F. von Höhnel, 1918
- Genus Dubitatio Spegazzini, 1882 accepted as Passerinula P.A. Saccardo, 1875
- Genus Enchnosphaeria Fuckel, 1870 accepted as Herpotrichia Fuckel, 1868
- Genus Farlowia P.A. Saccardo, 1883 accepted as Farlowiella P.A. Saccardo, 1891
- Genus Farlowiella P.A. Saccardo, 1891
- Genus Fusculina Crous & Summerell, 2006
- Genus Fusiformiseptata W. Dong, H. Zhang & K.D. Hyde in Dong et al., 2020
- Genus Harpocephalum G.F. Atkinson, 1897 accepted as Periconia Tode, 1791
- Genus Helicascus J. Kohlmeyer, 1969
- Genus Herpotrichia Fuckel, 1868
- Genus Herpotrichiopsis F. von Höhnel, 1914 accepted as Pyrenochaeta De Notaris, 1849
- Genus Hyalobelemnospora T. Matsushima, 1993
- Genus Immotthia M.E. Barr, 1987
- Genus Khekia Petrak, 1921 accepted as Herpotrichia Fuckel, 1868
- Genus Lasiophoma Naumov, 1916 accepted as Pyrenochaeta De Notaris, 1849
- Genus Leptophoma F. von Höhnel, 1915 accepted as Phoma P.A. Saccardo, 1880
- Genus Leptosphaerulina McAlpine, 1902
- Genus Letendraea P.A. Saccardo, 1880
- Genus Macrodiplodina F. Petrak, 1962 accepted as Ascochyta Libert, 1830
- Genus Macroplodiella Spegazzini, 1908 accepted as Phoma P.A. Saccardo, 1880
- Genus Macroventuria Van der Aa, 1971
- Genus Margaretbarromyces R.A. Mindell, R.S. Currah, R.A. Stockey & G. Beard in Mindell, Stockey, Beard & Currah, 2007 †
- Genus Medicopsis J. de Gruyter, G.J.M. Verkley & P.W. Crous in Gruyter, Woudenberg, Aveskamp, Verkley, Groenewald & Crous, 2012
- Genus Metameris Theissen & H. Sydow, 1915
- Genus Monoblastiopsis R.C. Harris & C.A. Morse, 2008
- Genus Mycocentrospora F.C. Deighton, 1972
- Genus Mycodidymella C.Z. Wei, Y. Harada & K. Katumoto, 1998
- Genus Neopeckia P.A. Saccardo, 1883
- Genus Neophaeosphaeria M.P.S. Câmara, M.E. Palm & A.W. Ramaley, 2003
- Genus Neopodoconis M.A. Rifai, 2008
- Genus Ochrocladosporium Crous & U. Braun, 2007
- Genus Pachytrichum H. Sydow, 1925 accepted as Periconia Tode, 1791
- Genus Paraliomyces Kohlmeyer, 1959
- Genus Paraphoma G. Morgan-Jones & J.F. White, 1983 accepted as Phoma P.A. Saccardo, 1880
- Genus Passerinula P.A. Saccardo, 1875
- Genus Periconia Tode, 1791
- Genus Phaeosphaeriopsis M.P.S. Câmara, M.E. Palm & A.W. Ramaley, 2003
- Species Phaeosphaeriopsis agavensis (A.W. Ramaley, M.E. Palm & M.E. Barr) M.P.S. Câmara, M.E. Palm & A.W. Ramaley, 2003
- Species Phaeosphaeriopsis glaucopunctata (Grev.) M.P.S. Câmara, M.E. Palm & A.W. Ramaley, 2003
- Species Phaeosphaeriopsis nolinae (A.W. Ramaley) M.P.S. Câmara, M.E. Palm & A.W. Ramaley, 2003
- Species Phaeosphaeriopsis obtusispora (Speg.) M.P.S. Câmara, M.E. Palm & A.W. Ramaley, 2003
- Genus Phaeostagonospora A.W. Ramaley, 1997
- Genus Phoma P.A. Saccardo, 1880
- Genus Phomopsina Petrak, 1922 accepted as Phoma P.A. Saccardo, 1880
- Genus Plenodomus Preuss, 1851 accepted as Phoma P.A. Saccardo, 1880
- Genus Pleocatenata Y.R. Sun, Y. Wang & K.D. Hyde, 2022
- Genus Podoconis Boedijn, 1933 accepted as Sporidesmium Link, 1809
- Genus Polyopeus A.S. Horne, 1920 accepted as Phoma P.A. Saccardo, 1880
- Genus Protocucurbitaria Naumov, 1951
- Genus Pseudochaetosphaeronema E. Punithalingam, 1979
- Genus Pseudodidymella C.Z. Wei, Y. Harada & K. Katumoto, 1997
- Genus Pseudohelminthosporium C. Phukhamsakda & K.D. Hyde, 2020 accepted as Neopodoconis M.A. Rifai, 2008
- Genus Pseudoplea F. von Höhnel, 1918 accepted as Leptosphaerulina McAlpine, 1902
- Genus Pseudopyrenidium P. Navarro-Rosinés, M.P. Zhurbenko & C. Roux, 2010
- Genus Pseudosclerophoma Petrak, 1923 accepted as Phoma P.A. Saccardo, 1880
- Genus Pseudosphaeria F. von Höhnel, 1907 accepted as Wettsteinina F. von Höhnel, 1907
- Genus Pseudotrichia Kirschstein, 1939
- Genus Pyrenochaeta De Notaris, 1849
- Genus Rhizosphaerella F. von Höhnel, 1917 accepted as Phoma P.A. Saccardo, 1880
- Genus Rhopographus Nitschke ex Fuckel, 1870
- Genus Scirrhodothis Theissen & H. Sydow, 1915 accepted as Metameris Theissen & H. Sydow, 1915
- Genus Scirrhophragma Theissen & H. Sydow, 1915 accepted as Metameris Theissen & H. Sydow, 1915
- Genus Sclerophomella F. von Höhnel, 1917 accepted as Phoma P.A. Saccardo, 1880
- Genus Sclerophomina F. von Höhnel, 1917 accepted as Phoma P.A. Saccardo, 1880
- Genus Scleropleella F. von Höhnel, 1918 accepted as Leptosphaerulina McAlpine, 1902
- Genus Setomelanoma M. Morelet, 1980
- Genus Setomelanomma M. Morelet, 1980
- Genus Shiraia Hennings, 1900
- Genus Sordariella J.N. Kapoor, S.P. Lal & Bahl, 1975 accepted as Herpotrichia Fuckel, 1868
- Genus Spegazzinula P.A. Saccardo, 1883 accepted as Passerinula P.A. Saccardo, 1875
- Genus Speira Corda, 1837
- Genus Sporidesmium Link, 1809
- Genus Sporocybe E.M. Fries, 1825 accepted as Periconia Tode, 1791
- Genus Sporodum Corda, 1837 accepted as Periconia Tode, 1791
- Genus Subbaromyces Hesseltine, 1953
- Genus Synphragmidium F. von Strauss in J. Sturm, 1853 accepted as Dictyosporium Corda, 1836
- Genus Tingoldiago K. Hirayama & K. Tanaka in Hirayama et al., 2010
- Genus Trichocephalum Costantin, 1888 accepted as Periconia Tode, 1791
- Genus Trinosporium P.W. Crous & C. Decock in Crous et al., 2012
- Genus Vialina Curzi, 1935 accepted as Phoma P.A. Saccardo, 1880
- Genus Wettsteinina F. von Höhnel, 1907
- Genus Wicklowia H.A. Raja, A. Ferrer & C.A. Shearer, 2010
- Genus Xenoberkleasmium N.G. Liu, J.K. Liu & K.D. Hyde, 2024
- Genus Xenobotryosphaeria W. Quaedvlieg, G.J.M. Verkley & P.W. Crous in Quaedvlieg, Verkley, Shin, Barreto, Alfenas, Swart, Groenewald & Crous, 2013
- Family Pseudoberkleasmiaceae Phukhamsakda & K.D. Hyde, 2019
- Family Pseudosphaeriaceae accepted as Pleosporales incertae sedis
- Family Pyrenophoraceae accepted as Pleosporaceae
- Family Sporormiaceae
- Family Sulcatisporaceae K. Tanaka & K. Hirayama, 2015
- Family Teichosporaceae M.E. Barr, 2002
- Family Testudinaceae
- Family Tetraplosphaeriaceae K. Tanaka & K. Hirayama, 2009
- Family Thyridariaceae Q. Tian & K.D. Hyde in Hyde et al., 2013
- Family Torulaceae A.K.J. Corda in Sturm, 1829
- Family Zopfiaceae
- 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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