• Microcoleus Desmazières ex Gomont, 1892
• Microcoleus acremannii Casamatta & Johansen, 2005
• Microcoleus acutirostris Gomont, 1892
• Microcoleus acutissimus N.L.Gardner, 1927 accepted as Trichocoleus acutissimus (N.L.Gardner) Anagnostidis, 2001
• Microcoleus acutissimus f. minor Bongale, 1987
• Microcoleus acutissimus var. colorata Bongale, 1987
• Microcoleus aitchinsonii Schaarschmidt, 1884
• Microcoleus amoenus (Gomont) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus amorphus Wolle ex Drouet, 1939
• Microcoleus amorphus Wolle, 1887 accepted as Microcoleus amorphus Wolle ex Drouet, 1939
• Microcoleus amplus N.L.Gardner, 1927
• Microcoleus amplus var. minor N.D.Kamat, 1963
• Microcoleus anguiformis Harvey ex Kirchner, 1898
• Microcoleus annulatus F.E.Fritsch & F.Rich, 1924
• Microcoleus antarcticus Casamatta & Johansen, 2005
• Microcoleus attenuatus (Fritsch) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus aurantiacus Hansgirg, 1892 accepted as Symplocastrum aurantiacum (Hansgirg) Anagnostidis, 2001
• Microcoleus autumnalis (Gomont) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus beggiatoiformis (Gomont) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus boergesenii (N.L.Gardner) Frémy, 1939 accepted as Blennothrix boergesenii (N.L.Gardner) Anagnostidis, 2001
• Microcoleus boryanus (Kützing) Rabenhorst, 1847 accepted as
• Microcoleus brasiliensis Borge, 1925
• Microcoleus burmanicus Desikachary, 1959
• Microcoleus calidus (Gomont ex Gomont) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus californicus Drouet, 1943
• Microcoleus cataractarum Hansgirg ex Forti, 1907
• Microcoleus caucasicus (Elenkin & Kosinskaja) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus cavanillesii González Guerrero, 1946 accepted as Trichocoleus cavanillesii (González Guerrero) Anagnostidis, 2001
• Microcoleus chthonoplastes Thuret ex Gomont, 1892 accepted as Coleofasciculus chthonoplastes (Thuret ex Gomont) M.Siegesmund, J.R.Johansen & T.Friedl, 2008
• Microcoleus chtonoplastes (Mertens) Zanardini
• Microcoleus codii Frémy, 1932
• Microcoleus confluens Setchell & N.L.Gardner, 1918 accepted as Blennothrix confluens (Setchell & N.L.Gardner) I.Umezaki, 1995
• Microcoleus corium (C.Agardh) Rabenhorst, 1847 accepted as Phormidium corium Gomont ex Gomont, 1892
• Microcoleus crustaceus (Voronichin) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus cryophilus Carlson, 1913
• Microcoleus curvatus Meneghini, 1842 accepted as Lyngbya curvata Rabenhorst ex Gomont, 1893
• Microcoleus delicatulus West & G.S.West, 1896 accepted as Trichocoleus delicatulus (West & G.S.West) Anagnostidis, 2001
• Microcoleus delicatulus var. attenuatus Ghose, 1927 accepted as Trichocoleus attenuatus (Ghose) Anagnostidis, 2001
• Microcoleus dillwynii Harvey, 1841 accepted as Desmonema dillwynii (Harvey) Berkeley & Thwaites, 1849
• Microcoleus erectiusculus Starmach, 1961 accepted as Trichocoleus erectiusculus (Starmach) Anagnostidis & Komárek, 2001
• Microcoleus evagineus González Guerrero (uncertain)
• Microcoleus favosus (Gomont) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus ferrugineus Frémy, 1937
• Microcoleus fonticola (Kirchner) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus friesii (C.Agardh) Thuret, 1875 accepted as Symplocastrum friesii (Gomont) Kirchner, 1898
• Microcoleus glaciei Johansen & Casamatta, 2005 accepted as Wilmottia murrayi (West & G.S.West) Strunecký, Elster & Komárek, 2011
• Microcoleus gracilis Hassall, 1845 (uncertain)
• Microcoleus granulatus Tutin, 1940
• Microcoleus grisea Thuret ex Bornet & Flahault, 1886
• Microcoleus guyanensis Crouan & Crouan, 1868 (uncertain)
• Microcoleus hiemalis (Jaag) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus hospita Hansgirg ex Forti, 1907 accepted as Trichocoleus hospita (Forti) Anagnostidis, 2001
• Microcoleus hospita var. eepilithicus Ercegovic, 1925
• Microcoleus howellii Setchell & Gardner, 1937
• Microcoleus hyalinus (Kützing) Kirchner, 1878 (uncertain)
• Microcoleus irriguus (Gomont) Drouet, 1968 accepted as Phormidium irriguum (Kützing ex Gomont) Anagnostidis & Komárek, 1988
• Microcoleus ivlevii Cado, 1958
• Microcoleus lacustris Farlow ex Gomont, 1892
• Microcoleus lacustris f. intermedius Vasishta, 1961
• Microcoleus lacustris f. minor Desikachary, 1959
• Microcoleus lauterbachii Schmidle, 1897
• Microcoleus limbatus (Harvey) Bornet, 1888 (uncertain)
• Microcoleus lyngbyaceus (Gomont) Drouet, 1968 accepted as Blennothrix lyngbyacea (Kützing ex Gomont) Anagnostidis & Komárek, 1988
• Microcoleus lyngbyei (Kützing) P.Crouan & H.Crouan, 1867 (uncertain)
• Microcoleus majusculus C.K.Tseng & M.Hua, 1984
• Microcoleus manshuriense Noda, 1963 (uncertain)
• Microcoleus membranaceus Kützing ex Rabenhorst, 1847 accepted as Phormidium autumnale Gomont, 1892 accepted as Microcoleus autumnalis (Gomont) Strunecky, Komárek & J.R.Johansen, 2013
• Microcoleus meneghinianus (Kützing) Rabenhorst, 1847 accepted as Phormidium meneghinianum Kützing ex Gomont, 1892
• Microcoleus minimus Frémy, 1930 accepted as Trichocoleus minimus (Frémy) Anagnostidis, 2001
• Microcoleus paludosus Gomont, 1892
• Microcoleus paludosus var. acuminatus N.L.Gardner, 1927
• Microcoleus pannosus (Bory) Rabenhorst, 1847 accepted as
• Microcoleus plantae Forti, 1907
• Microcoleus polythrix Hansgirg, 1890 accepted as Trichocoleus polythrix (Forti) Anagnostidis, 2001
• Microcoleus pseudautumnalis Y.Niiyama & A.Tuji, 2019
• Microcoleus purpureus N.L.Gardner, 1927
• Microcoleus repens (C.Agardh) Harvey, 1841 accepted as Oscillatoria repens C.Agardh ex Gomont, 1892
• Microcoleus rupicola (Tilden) F.E.Drouet, 1943 accepted as Schizothrix rupicola Tilden, 1896
• Microcoleus rushfortii Johansen & Casamatta, 2005
• Microcoleus salinus (Kützing) Montagne, 1851 (uncertain)
• Microcoleus sampaianus J.Sampaio, 1941
• Microcoleus sanctae-crucis Frémy, 1939 accepted as Trichocoleus sanctae-crucis (Frémy) Anagnostidis, 2001
• Microcoleus setchellianus (Gomont) Strunecky, Komárek & Johansen, 2013
• Microcoleus sikkimensis Santra, 1984
• Microcoleus sinensis C.-C.Jao, 1939
• Microcoleus sociatus West & G.S.West, 1897 accepted as Trichocoleus sociatus (West & G.S.West) Anagnostidis, 2001
• Microcoleus sociatus var. abiscoensis Skuja, 1964 accepted as Trichocoleus abiscoensis (Skuja) Komárek & Kovacik, 2013
• Microcoleus sociatus var. minor N.L.Gardner, 1927 accepted as Trichocoleus minor (N.L.Gardner) Anagnostidis, 2001
• Microcoleus sociatus var. tenuis Behre, 1953
• Microcoleus steenstrupii J.B.Petersen, 1923
• Microcoleus subandinus Schwabe, 1944
• Microcoleus subsalsus (Gomont) Strunecky, Komárek & Johansen, 2013
• Microcoleus subtorulosus Gomont ex Gomont, 1892
• Microcoleus subtorulosus var. rupestris Y.Li, 1989
• Microcoleus tenerrimus Gomont, 1892 accepted as Trichocoleus tenerrimus (Gomont) Anagnostidis, 2001
• Microcoleus thermalis Vouk, 1916 accepted as Trichocoleus thermalis (V.Vouk) Anagnostidis, 2001
• Microcoleus thomensis P.Sampaio, 1958
• Microcoleus tisserantii Frémy, 1930
• Microcoleus vaginatus Gomont, 1892
• Microcoleus vaginatus f. monticola (Gomont) Elenkin