Between brackets is the number of accepted species
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- Biota
- Kingdom Animalia
- Kingdom Archaea
- Kingdom Bacteria
- Kingdom Chromista
- Kingdom Fungi
- Kingdom Plantae
- Kingdom Protista accepted as Protozoa
- Kingdom Protozoa
- Subkingdom Eozoa
- Subkingdom Sarcomastigota
- Phylum Amoebozoa
- Subphylum Conosa
- Subphylum Eumycetozoa
- Class Ceratiomyxomycetes
- Class Dictyostelia accepted as Dictyosteliomycetes
- Class Dictyosteliomycetes
- Class Myxomycetes
- Order Clastodermatales
- Order Cribrariales
- Order Echinosteliales
- Order Echinosteliida accepted as Echinosteliales
- Order Echinosteliopsidales
- Order Fuscisporida accepted as Myxomycetes
- Order Liceales
- Order Liceida accepted as Liceales
- Order Meridermatales
- Order Physarales
- Family Didymiaceae Rostafiński, 1873 ex Cooke, 1877
- Genus Amphisporium Link, 1815 accepted as Didymium H.A. Schrader, 1797
- Genus Carcerina E.M. Fries, 1849 accepted as Diderma Persoon, 1794
- Genus Chondrioderma Rostafinski, 1873 accepted as Diderma Persoon, 1794
- Species Chondrioderma asteroides Lister & G. Lister, 1902 accepted as Diderma asteroides (Lister & G. Lister) G. Lister, 1911
- Species Chondrioderma cinereum (Morgan) Sacc. & P. Syd., 1908 accepted as Diderma cinereum Morgan, 1894
- Species Chondrioderma contextum (Pers.) Rostaf., 1873 accepted as Physarum contextum (Pers.) Pers., 1801
- Species Chondrioderma crustaceum (Peck) Berl., 1888 accepted as Diderma crustaceum Peck, 1874
- Species Chondrioderma deplanatum (Fr.) Rostaf., 1876 accepted as Diderma deplanatum Fr., 1829
- Species Chondrioderma difforme (Pers.) Rostaf., 1873 accepted as Didymium difforme (Pers.) Gray, 1821
- Species Chondrioderma floriforme (Bull.) Rostaf., 1875 accepted as Diderma floriforme (Bull.) Pers., 1794
- Species Chondrioderma globosum (Pers.) Rostaf., 1875 accepted as Diderma globosum Pers., 1794
- Species Chondrioderma hemisphaericum (Bull.) Torrend, 1908 accepted as Diderma hemisphaericum (Bull.) Hornem., 1829
- Species Chondrioderma lucidum (Berk. & Broome) Cooke, 1877 accepted as Diderma lucidum Berk. & Broome, 1861
- Species Chondrioderma lyallii Massee, 1892 accepted as Diderma lyallii (Massee) T. Macbr., 1899
- Species Chondrioderma michelii (Lib.) Rostaf., 1873 accepted as Diderma hemisphaericum (Bull.) Hornem., 1829
- Species Chondrioderma montanum Meyl., 1910 accepted as Diderma montanum (Meyl.) Meyl., 1921
- Species Chondrioderma niveum Rostaf., 1874 accepted as Diderma niveum (Rostaf.) T. Macbr., 1899
- Species Chondrioderma radiatum Rostaf., 1875 accepted as Diderma radiatum (L.) Morgan, 1894
- Species Chondrioderma reticulatum Rostaf., 1875 accepted as Diderma effusum (Schwein.) Morgan, 1894
- Species Chondrioderma sauteri Rostaf., 1874 accepted as Diderma sauteri (Rostaf.) T. Macbr., 1899
- Species Chondrioderma simplex J. Schröt., 1885 accepted as Diderma simplex (J. Schröt.) G. Lister, 1911
- Species Chondrioderma spumarioides (Fr.) Rostaf., 1873 accepted as Diderma spumarioides (Fr.) Fr., 1829
- Species Chondrioderma testaceum (Schrad.) Rostaf., 1874 accepted as Diderma testaceum (Schrad.) Pers., 1801
- Species Chondrioderma trevelyani (Grev.) Rostaf., 1874 accepted as Diderma trevelyani (Grev.) Fr., 1829
- Species Chondrioderma vaccinum (Durieu & Mont.) Rostaf., 1874 accepted as Didymium vaccinum (Durieu & Mont.) Buchet, 1920
- Genus Cionium Link, 1809 accepted as Didymium H.A. Schrader, 1797
- Genus Diderma Persoon, 1794
- Genus Didymium H.A. Schrader, 1797
- Genus Disporium Leman in F. Cuvier, 1819 accepted as Didymium H.A. Schrader, 1797
- Genus Leangium Link, 1809 accepted as Diderma Persoon, 1794
- Genus Lepidoderma de Bary in Rostafinski, 1873
- Genus Lepidodermopsis F. von Höhnel, 1909 accepted as Didymium H.A. Schrader, 1797
- Genus Lepidodermopsis Wilczek & Meylan, 1934 accepted as Lepidoderma de Bary in Rostafinski, 1873
- Genus Lignyota E.M. Fries, 1849
- Genus Mucilago Battarra, 1755
- Genus Polychysmium Léveillé, 1846 accepted as Diderma Persoon, 1794
- Genus Polyschismium Corda, 1842 accepted as Diderma Persoon, 1794
- Genus Pseudodidymium R. Michel, Walochnik & Aspöck, 2003 accepted as Didymium H.A. Schrader, 1797
- Genus Spumaria Persoon in J.F. Gmelin, 1792 accepted as Mucilago Battarra, 1755
- Genus Spumaria Persoon, 1792 accepted as Mucilago Battarra, 1755
- Genus Squamuloderma D.T. Kowalski, 1973 accepted as Didymium H.A. Schrader, 1797
- Genus Wilczekia Meylan, 1925 accepted as Diderma Persoon, 1794
- Family Didymiidae accepted as Didymiaceae Rostafiński, 1873 ex Cooke, 1877
- Family Elaeomyxaceae Hagelstein, 1942 ex M.L. Farr & H.W. Keller, 1982 accepted as Lamprodermataceae T. Macbride, 1899
- Family Elaeomyxidae accepted as Elaeomyxaceae Hagelstein, 1942 ex M.L. Farr & H.W. Keller, 1982
- Family Lamprodermataceae T. Macbride, 1899
- Family Lamprodermidae accepted as Lamprodermataceae T. Macbride, 1899
- Family Physaraceae Chevallier, 1826
- Family Physaridae accepted as Physaraceae Chevallier, 1826
- Genus Diachaeella F. von Höhnel, 1909 accepted as Diachea E.M. Fries, 1825
- Genus Tasmaniomyxa S.J. Lloyd, D.V. Leontyev, G. Moreno, Á. López Villalba & M. Schnittler, 2024
- Order Reticulariales
- Order Stemonitales accepted as Stemonitidales
- Order Stemonitidales
- Order Trichiales
- Order Trichiida accepted as Trichiales
- Family "Merodermid clade" accepted as Meridermatales
- Family Minakatellaceae Nannenga-Bremekamp 1982, 1985 ex Neubert et al., 1993 accepted as Myxomycetes
- Family Minakatellidae accepted as Minakatellaceae Nannenga-Bremekamp 1982, 1985 ex Neubert et al., 1993
- Genus Amylotrogus E. Roze, 1896
- Genus Arcyriatella E. Hochgesand & G. Gottsberger, 1989
- Genus Calonema Morgan, 1893
- Genus Calyssosporium A.C.J. Corda in J. Sturm, 1831
- Genus Clathrodastrum O. Kuntze, 1891 accepted as Clathroidastron Adanson, 1763
- Genus Clathroidastron Adanson, 1763
- Genus Clathroïdastron Adanson, 1763 accepted as Clathroidastron Adanson, 1763
- Genus Coniocephalum Brondeau, 1828
- Genus Demordium Link, 1809 accepted as Dermodium Link, 1809
- Genus Dermodium Link, 1809
- Genus Diachea E.M. Fries, 1825
- Genus Halterophora Endlicher, 1836
- Genus Henningsinia A. Möller, 1901
- Genus Hystricapsa Preuss, 1851
- Genus Leptoderma G. Lister, 1913
- Genus Microcarpon Schrader ex J.F. Gmelin in Gmelin, 1792
- Genus Minakatella G. Lister, 1921
- Genus Mycosphaeroides T.N. Hermann in Sokolov, 1979 †
- Genus Myrosporium A.J. Corda in J. Sturm, 1831
- Genus Myxomyces Salimbeni, 1920
- Genus Myxomycetes Renault, 1895 †
- Genus Myxomycites Meschinelli, 1898 † accepted as Myxomycetes Renault, 1895 †
- Genus Ostracococcum Wallroth, 1833
- Genus Paleoarcyria M. Jacques-Félix, C.N. Miller & M.V. Locquin, 1983
- Genus Paradiachea Hertel, 1956
- Genus Pecila Lepelletier, 1822
- Genus Phlebomorpha Persoon, 1822
- Genus Protophysarum M. Blackwell & Alexopoulos, 1975
- Genus Stylonites E.M. Fries, 1848
- Genus Tipularia F.F. Chevallier, 1822 accepted as Halterophora Endlicher, 1836
- Genus Trabrooksia H.W. Keller, 1980
- Genus Trichioides Y.K. Novozhilov, H. van Hooff & M. Jagers, 2014
- Genus Xyloidium Czerniaiev, 1845
- Subphylum Lobosa
- Class Amoebozoa
- Class Amoebozoa incertae sedis
- Order Stereomyxida accepted as Amoebozoa incertae sedis
- Phylum Choanozoa
- Phylum Cryptomycota accepted as Choanozoa
- Phylum Sarcomastigota (awaiting allocation)
- Phylum Sulcozoa
- Subkingdom Zoomastigophora accepted as Sarcomastigota
- Phylum Hemimastigophora
- Phylum Nebulidia
- Phylum Nibbleridia
- Phylum Protozoa incertae sedis
- Phylum Rhizopoda accepted as Sarcomastigota
- Phylum Sarcomastigophora accepted as Sarcomastigota
- Class Mastigophora accepted as Sarcomastigota
- Class Protozoa (awaiting allocation)
- Genus Megaclonophycus Xue, Tang, Yu & Zhou, 1995 †
- Genus Megasphaera Chen & Liu, 1986 †
- Genus Parapandorina Xue, Tang, Yu & Zhou, 1995 †
- Genus Syssomonas Tikhonenkov, Hehenberger, Mylnikov & Keeling in Hehenberger et al., 2017
- Genus Tianzhushania L.M. Yin & Z.P. Li, 1978 †
- Genus Tunicaraptor Tikhonenkov et al., 2020
- Genus Yinitianzhushania S. Xiao, C. Zhou, P. Liu, D. Wang & X. Yuan, 2014 †
- Kingdom Viruses
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