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
- Order Pezizales
- Family Aleuriaceae accepted as Pezizaceae
- Family Ascobolaceae
- Family Ascodesmidaceae
- Family Caloscyphaceae
- Family Carbomycetaceae
- Family Chorioactidaceae
- Family Discinaceae
- Family Geneaceae accepted as Pyronemataceae
- Family Glaziellaceae
- Family Glischodermataceae accepted as Pezizaceae
- Family Glischrodermataceae accepted as Pezizaceae
- Family Helvellaceae
- Family Hemiascosporiaceae accepted as Ascodesmidaceae
- Family Humariaceae accepted as Pyronemataceae
- Family Karstenellaceae
- Family Morchellaceae
- Family Mycogalopsidaceae accepted as Pyronemataceae
- Family Otideaceae accepted as Pyronemataceae
- Family Otidiaceae accepted as Pyronemataceae
- Family Pezizaceae
- Family Pezizales incertae sedis
- Family Pyronemataceae
- Genus Acervus Kanouse, 1938
- Genus Actinospora Ingold, 1952 accepted as Actinosporella E. Descals, L. Marvanová & J. Webster, 1999
- Genus Actinosporella E. Descals, L. Marvanová & J. Webster, 1999
- Genus Aleuria (E.M. Fries) Fuckel, 1870
- Genus Aleurina Massee, 1898
- Genus Angiophaeum P.A. Saccardo, 1898 accepted as Phaeangium Patouillard, 1894
- Genus Anixia H. Hoffmann, 1862 accepted as Orbicula M.C. Cooke, 1871
- Genus Anthracobia Boudier, 1885
- Genus Aparaphysaria Spegazzini, 1922
- Genus Arpinia P. Berthet, 1974
- Genus Ascocalathium Eidam ex J. Schröter, 1893
- Genus Ascorhizoctonia Chin S. Yang & Korf, 1985
- Genus Ascosparassis Kobayasi, 1960
- Genus Ascosporassis
- Genus Barlaea P.A. Saccardo, 1889 accepted as Lamprospora De Notaris, 1863
- Genus Barlaeina P.A. Saccardo & P. Sydow, 1899 accepted as Lamprospora De Notaris, 1863
- Genus Boudierella P.A. Saccardo in Marchal, 1895
- Genus Byssonectria P.A. Karsten, 1881
- Genus Chaetothiersia B.A. Perry & Pfister, 2007
- Genus Chalazion H. Dissing & S. Sivertsen, 1975
- Genus Cheilymenia Boudier, 1885
- Genus Ciliaria Quélet in Boudier, 1885 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Cochlearia (M.C. Cooke) Lambotte, 1888 accepted as Otidea (Persoon) Bonorden, 1851
- Genus Complexipes C. Walker, 1979
- Genus Coprobia Boudier, 1885 accepted as Cheilymenia Boudier, 1885
- Genus Crouania Fuckel, 1870 accepted as Lamprospora De Notaris, 1863
- Genus Densocarpa Gilkey, 1954 accepted as Stephensia Tulasne, 1845
- Genus Dichobotrys G.L. Hennebert, 1973
- Genus Dictyocoprotus J.C. Krug & R.S. Khan, 1991
- Genus Discomycetella Sanwal, 1953 accepted as Miladina M. Svrček, 1972
- Genus Elderia McLennan, 1961 accepted as Stephensia Tulasne, 1845
- Genus Eoaleurina R.P. Korf & W.-Y. Zhuang in W.-Y. Zhuang & R.P. Korf, 1986
- Genus Fimaria Velenovský, 1934 accepted as Pseudombrophila Boudier, 1885
- Genus Flavoscypha H. Harmaja, 1974 accepted as Otidea (Persoon) Bonorden, 1851
- Genus Galeoscypha M. Svrček & J. Moravec, 1989
- Genus Genabea L.R. Tulasne & C. Tulasne, 1844 accepted as Genea Vittadini, 1831
- Genus Genea Vittadini, 1831
- Genus Geneosperma Rifai, 1968
- Genus Geopora Harkness, 1885
- Genus Geopyxis (Persoon) P.A. Saccardo, 1889
- Genus Gilkeya M.E. Smith, Trappe & Rizzo, 2007
- Genus Greletia J.C. Donadini, 1980 accepted as Smardaea M. Svrček, 1969
- Genus Hiemsia M. Svrček, 1969
- Genus Hoffmannoscypha B. Stielow, M. Göker & H.P. Klenk in Stielow, Hensel, Strobelt, Makonde, Rohde, Dijksterhuis, Klenk & Göker, 2012
- Genus Humaria Fuckel, 1870
- Genus Humaria (E.M. Fries) Boudier, 1885 accepted as Octospora J. Hedwig, 1789
- Genus Humariella J. Schröter in Cohn, 1893 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Humarina Seaver, 1927 accepted as Octospora J. Hedwig, 1789
- Genus Hydnocaryon Wallroth, 1833 accepted as Genea Vittadini, 1831
- Genus Hydnocystis L.R. Tulasne, 1844
- Genus Hypotarzetta J.-C. Donadini, 1985
- Genus Inermisia Rifai, 1968 accepted as Byssonectria P.A. Karsten, 1881
- Genus Jafnea R.P. Korf, 1960
- Genus Jafneadelphus Rifai, 1968 accepted as Aleurina Massee, 1898
- Genus Kotlabaea M. Svrček, 1969
- Genus Lachnea (E.M. Fries) Gillet, 1879 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Lachnea Boudier, 1885 accepted as Humaria Fuckel, 1870
- Genus Lamprospora De Notaris, 1863
- Genus Lasiobolidium D.W. Malloch & R.F. Cain, 1971
- Genus Lathraeodiscus H. Dissing & S. Sivertsen, 1989
- Genus Lazuardia M.A. Rifai, 1988
- Genus Leucoloma Fuckel, 1870 accepted as Octospora J. Hedwig, 1789
- Genus Leucopezis F.E. Clements, 1909 accepted as Humaria Fuckel, 1870
- Genus Leucoscypha Boudier, 1885
- Genus Luciotrichus R. Galán & A. Raitviir, 1995
- Genus Melastiza Boudier, 1885
- Genus Melastiziella Svrček, 1948 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Micronematobotrys X. Sun & L.D. Guo, 2010
- Genus Miladina M. Svrček, 1972
- Genus Monascella J. Guarro & J.A. von Arx, 1986
- Genus Moravecia D. Benkert, M. Caillet & G. Moyne, 1987
- Genus Mycogala Rostafinski ex P.A. Saccardo, 1884 accepted as Orbicula M.C. Cooke, 1871
- Genus Mycogalopsis Gjurašin, 1925
- Genus Mycolachnea Maire, 1937 accepted as Humaria Fuckel, 1870
- Genus Myrmecocystis H.W. Harkness, 1899 accepted as Genea Vittadini, 1831
- Genus Nannfeldtiella Eckblad, 1968 accepted as Pseudombrophila Boudier, 1885
- Genus Neottiella (M.C. Cooke) P.A. Saccardo, 1889
- Genus Neottiopezis F.E. Clements, 1903 accepted as Neottiella (M.C. Cooke) P.A. Saccardo, 1889
- Genus Nothojafnea Rifai, 1968
- Genus Octospora J. Hedwig, 1789
- Genus Octosporella P. Döbbeler, 1980
- Genus Orbicula M.C. Cooke, 1871
- Genus Otidea (Persoon) Bonorden, 1851
- Genus Otideopsis B. Liu & J.-Z. Cao, 1987
- Species Otideopsis kaushalii (J. Moravec) J. Moravec, 1988
- Species Otideopsis yunnanensis B. Liu & J.Z. Cao, 1987
- Genus Oviascoma Y.J. Yao & B.M. Spooner, 1996
- Genus Parascutellinia M. Svrček, 1975
- Genus Paratrichophaea G. Trigaux, 1985
- Genus Patella F.H. Wiggers ex Seaver, 1928 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Petchiomyces E. Fischer & Mattirolo, 1938
- Genus Peziza Fuckel, 1870 accepted as Aleuria (E.M. Fries) Fuckel, 1870
- Genus Phaeangium Patouillard, 1894
- Genus Phaedropezia Le Gal, 1953 accepted as Acervus Kanouse, 1938
- Genus Phycoascus A. Møller, 1901 accepted as Pyronema Carus, 1835
- Genus Protogenea Kobayasi, 1964 accepted as Hydnocystis L.R. Tulasne, 1844
- Genus Pseudaleuria D.E. Lusk, 1987
- Genus Pseudhydnotrya E. Fischer in Engler & Prantl, 1897 accepted as Geopora Harkness, 1885
- Genus Pseudocollema Kanouse & A.H. Smith, 1940 accepted as Byssonectria P.A. Karsten, 1881
- Genus Pseudogenea Buchholz, 1901 accepted as Genea Vittadini, 1831
- Genus Pseudohydnotrya E. Fischer, 1897 accepted as Geopora Harkness, 1885
- Genus Pseudombrophila Boudier, 1885
- Genus Pseudotis (Boudier) Boudier, 1907 accepted as Otidea (Persoon) Bonorden, 1851
- Genus Pustularia Fuckel, 1870 accepted as Tarzetta (M.C. Cooke) Lambotte, 1828
- Genus Pustulina Eckblad, 1968 accepted as Tarzetta (M.C. Cooke) Lambotte, 1828
- Genus Pyronema Carus, 1835
- Genus Pyropyxis K.N. Egger, 1984
- Genus Ramsbottomia W.D. Buckley, 1923
- Genus Ramulina Velenovský, 1947 accepted as Pseudombrophila Boudier, 1885
- Genus Rhizoblepharia M.A. Rifai, 1968
- Genus Rhodoscypha H. Dissing & S. Sivertsen, 1983
- Genus Rhodotarzetta H. Dissing & S. Sivertsen, 1983
- Genus Rubelia Nieuwland, 1916 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Sepultaria (M.C. Cooke) Boudier, 1885 accepted as Geopora Harkness, 1885
- Genus Sepultariella Kutorga, 2000 accepted as Sepultariella N. Van Vooren, U. Lindemann & R. Healy, 2017
- Genus Sepultariella N. Van Vooren, U. Lindemann & R. Healy, 2017
- Genus Smardaea M. Svrček, 1969
- Genus Smarodsia Raitviir & Vimba, 2006
- Genus Sowerbyella Nannfeldt, 1938
- Genus Sphaeriopsis H.T. Geyler in N.A.E. von Nordenskiöld, 1887 †
- Genus Sphaerosoma Klotzsch in A. Dietrich, 1839
- Genus Sphaerospora (P.A. Saccardo) P.A. Saccardo, 1889 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Sphaerosporella (Svrček) Svrček & Kubička, 1961
- Genus Sphaerosporula O. Kuntze, 1898 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Sphaerozosma Corda, 1842 accepted as Sphaerosoma Klotzsch in A. Dietrich, 1839
- Genus Spooneromyces T. Schumacher & J. Moravec, 1989
- Genus Stephensia Tulasne, 1845
- Genus Stereolachnea F. von Höhnel, 1917 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Svrcekomyces J. Moravec, 1976 accepted as Pseudombrophila Boudier, 1885
- Genus Tarzetta (M.C. Cooke) Lambotte, 1828
- Genus Trichaleurina H. Rehm, 1903 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Trichaleuris F.E. Clements, 1909 accepted as Scutellinia (M.C. Cooke) Lambotte, 1888
- Genus Tricharia Boudier, 1885 accepted as Tricharina Eckblad, 1968
- Genus Tricharina Eckblad, 1968
- Genus Trichophaea Boudier, 1885
- Genus Trichophaeopsis R.P. Korf & R.W. Erb, 1972
- Genus Trichopheae
- Genus Warcupia J.W. Paden & J.V. Cameron, 1972
- Genus Wenyingia Z. Wang & D.H. Pfister, 2001
- Genus Wilcoxina Chin S. Yang & Korf, 1985
- Family Rhizinaceae
- Family Sarcoscyphaceae
- Family Sarcosomataceae
- Family Terfeziaceae accepted as Pezizaceae
- Family Tuberaceae
- Order Pezizomycetes incertae sedis
- 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 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 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 Rhyniomycelium M. Krings & C.J. Harper, 2023 †
- Kingdom Plantae
- Kingdom Protista accepted as Protozoa
- Kingdom Protozoa
- Kingdom Viruses
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