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
- Phylum Basidiobolomycota accepted as Zygomycota
- Phylum Basidiomycota
- Class Agaricomycetes
- Order Agaricales
- Family Agaricaceae
- Family Agaricales incertae sedis
- Family Amanitaceae E.-J. Gilbert, 1940
- Family Arachniaceae accepted as Agaricaceae
- Family Asterogastraceae accepted as Hydnangiaceae
- Family Biannulariaceae W. Jülich, 1981
- Family Bolbitiaceae
- Family Broomeiaceae
- Family Callistosporiaceae A. Vizzini, G. Consiglio, M. Marchetti & P. Alvarado, 2020
- Family Clavariaceae
- Family Clitocybaceae A. Vizzini, G. Consiglio & M. Marchetti, 2020
- Family Coprinaceae accepted as Agaricaceae
- Family Cortinariaceae
- Family Cribbeaceae accepted as Cortinariaceae
- Family Cribbiaceae accepted as Cortinariaceae
- Family Cyphellaceae
- Family Entolomataceae
- Family Fistulinaceae
- Family Gigaspermataceae Jülich, 1981 accepted as Cortinariaceae
- Family Hemigasteraceae
- Family Hemigastraceae accepted as Hemigasteraceae
- Family Hydnangiaceae
- Family Hygrophoraceae
- Family Hymenogasteraceae accepted as Strophariaceae
- Family Hymenogastraceae accepted as Strophariaceae
- Family Inocybaceae
- Family Lepiotaceae accepted as Agaricaceae
- Family Lycoperdaceae F. Berchtold & J.S. Presl,1820
- Family Lyophyllaceae
- Family Marasmiaceae
- Family Mycenaceae
- Family Mycenastraceae accepted as Agaricaceae
- Family Mycospongiaceae accepted as Agaricales incertae sedis
- Family Niaceae Jülich, 1982
- Family Nidulariaceae accepted as Agaricaceae
- Family Omphalotaceae A. Bresinsky, 1985
- Family Palaeoclavariaceae †
- Family Phelloriniaceae
- Family Physalacriaceae
- Family Pleurotaceae
- Family Pluteaceae
- Family Podaxaceae accepted as Agaricaceae
- Family Porotheleaceae Murrill, 1916
- Family Psathyrellaceae
- Family Pterulaceae
- Family Rhodophyllaceae accepted as Entolomataceae
- Family Schizophyllaceae
- Family Secotiaceae accepted as Agaricaceae
- Family Strophariaceae
- Family Torrendiaceae accepted as Amanitaceae E.-J. Gilbert, 1940
- Family Tricholomataceae
- Family Tulostomataceae accepted as Agaricaceae
- Family Typhulaceae
- Genus Astoma S.F. Gray, 1821 accepted as Sclerotium Tode, 1790
- Genus Cnazonaria Corda in J. Sturm, 1829 accepted as Typhula (Persoon) E.M. Fries, 1818
- Genus Coccopleum Ehrenberg, 1818 accepted as Sclerotium Tode, 1790
- Genus Dacryopsella F. von Höhnel, 1915 accepted as Pistillina Quélet, 1880
- Genus Gliocoryne R. Maire ex Guinier & R. Maire, 1909 accepted as Pistillaria E.M. Fries, 1821
- Genus Lutypha I.P.S. Khurana, K.S. Thind & J. Berthier, 1977
- Species Lutypha sclerotiophila Khurana, K.S. Thind & Berthier, 1977
- Genus Macrotyphula R.H. Petersen, 1972
- Genus Phacorhiza Persoon, 1822 accepted as Typhula (Persoon) E.M. Fries, 1818
- Genus Pistillaria E.M. Fries, 1821
- Genus Pistillina Quélet, 1880
- Genus Scleromitra Corda in J. Sturm, 1829 accepted as Pistillaria E.M. Fries, 1821
- Genus Sclerotiomyces Woronichin, 1926 accepted as Sclerotium Tode, 1790
- Genus Sclerotium Tode, 1790
- Genus Sphaerula Patouillard, 1883 accepted as Pistillaria E.M. Fries, 1821
- Genus Typhula (Persoon) E.M. Fries, 1818
- Genus Xylochoeras E.M. Fries, 1849 accepted as Sclerotium Tode, 1790
- Family Volvariaceae accepted as Pluteaceae
- Family Xerulaceae accepted as Physalacriaceae
- Genus Annularia Rafinesque, 1815
- Order Agaricomycetes incertae sedis
- Order Agaricomycetidae incertae sedis
- Order Atheliales
- Order Auriculariales
- Order Boletales
- Order Cantharellales
- Order Corticiales
- Order Geastrales
- Order Gloeophyllales
- Order Gomphales
- Order Hymenochaetales
- Order Hysterangiales
- Order Phallales
- Order Polyporales
- Order Russulales
- Order Sebacinales
- Order Sistotremastrales
- Order Thelephorales
- Order Trechisporales
- Class Agaricostilbomycetes
- Class Atractiellomycetes
- Class Basidiomycota incertae sedis
- Class Classiculomycetes
- Class Cryptomycocolacomycetes
- Class Cystobasidiomycetes
- Class Dacrymycetes
- Class Entorrhizomycetes
- Class Exobasidiomycetes
- Class Geminibasidiomycetes
- Class Microbotryomycetes
- Class Mixiomycetes
- Class Pucciniomycetes
- Class Tremellomycetes
- Class Tritirachiomycetes
- Class Ustilaginomycetes
- Class Wallemiomycetes
- 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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