1. Species Microcystis aeruginosa (Kützing) Kützing, 1846
2. Species Microcystis amethystina (Filarszky) Forti, 1907
3. Species Microcystis argentea J.Schiller, 1954
4. Species Microcystis bengalensis Banerjii, 1936
5. Species Microcystis botrys Teiling, 1942
6. Species Microcystis comperei Komárek, 1984
7. Species Microcystis complanata Skuja, 1964
8. Species Microcystis densa G.S.West, 1909
9. Species Microcystis dimidiata (Kützing) P.C.Silva, 1996
10. Species Microcystis dimorpha Joosten, 2006
11. Species Microcystis donnellii Wolle, 1879
12. Species Microcystis elabentoides Zalessky, 1926
13. Species Microcystis elongata Desikachary, 1959
14. Species Microcystis exigua M.D.Zalessky, 1926
15. Species Microcystis firma (Kützing) Schmidle, 1902
16. Species Microcystis flosaquae (Wittrock) Kirchner, 1898
17. Species Microcystis flos-aquae (Wittrock) Kirchner, 1898
18. Species Microcystis fuscolutea (Hansgirg) Forti, 1907
19. Species Microcystis grevillii
20. Species Microcystis ichthyoblabe (G.Kunze) Kützing, 1843
21. Species Microcystis lamelliformis Holsinger, 1954
22. Species Microcystis lutescens J.Schiller, 1954
23. Species Microcystis marginata (Meneghini) Kützing, 1846
24. Species Microcystis maxima C.Bernard, 1908
25. Species Microcystis merismopedioides F.E.Fritsch, 1912
26. Species Microcystis natans Lemmermann ex Skuja, 1934
27. Species Microcystis novacekii (Komárek) Compère, 1974
28. Species Microcystis ochracea (Brand) Lemmermann, 1907
29. Species Microcystis orissica West, 1911
30. Species Microcystis ovalis Hollenberg, 1939
31. Species Microcystis panniformis Komárek, Komárková-Legnerová, Sant'Anna, M.T.P.Azevedo & P.A.C.Senna, 2002
32. Species Microcystis prasina (Wittrock) Lemmermann, 1904
33. Species Microcystis protocystis W.B.Crow, 1923
34. Species Microcystis protogenita (Biasoletto) Rabenhorst, 1865
35. Species Microcystis pseudofilamentosa W.B.Crow, 1923
36. Species Microcystis pulverea (H.C.Wood) Forti, 1907
37. Species Microcystis ramosa Bharadwaya, 1935
38. Species Microcystis reticulata Lemmermann
39. Species Microcystis robusta (H.W.Clark) Nygaard, 1925
40. Species Microcystis rosea Kufferath, 1942
41. Species Microcystis scripta (P.Richter) Lemmermann, 1903
42. Species Microcystis smithii Komárek & Anagnostidis, 1995
43. Species Microcystis splendens Hollenberg, 1939
44. Species Microcystis supersalsa J.Schiller, 1956
45. Species Microcystis thermalis Yoneda, 1938
46. Species Microcystis toxica E.L.Stephens, 1948
47. Species Microcystis viridis (A.Braun) Lemmermann, 1903
48. Species Microcystis wesenbergii (Komárek) Komárek ex Komárek, 2006
49. Species Microcystis zanardinii (Hauck) P.Silva, 1996
50. Species Microcystis zanardinii. (Hauck) P. Silva
51. Species Microcystis anodontae (Hansgirg) Elenkin, 1938 accepted as Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865 (synonym)
52. Species Microcystis atra Kützing, 1833 accepted as Gloeocapsa atrata Kützing, 1843 (synonym)
53. Species Microcystis biformis (A.Braun) Bourrelly, 1970 accepted as Aphanocapsa biformis A.Braun, 1879 (synonym)
54. Species Microcystis calciphila Schwabe, 1947 accepted as Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865 (synonym)
55. Species Microcystis clarionensis (Setchell & N.L.Gardner) J.De Toni, 1938 accepted as Chlorogloea clarionensis (Setchell & N.L.Gardner) Beljakova, 2010
56. Species Microcystis concharum (Hansgirg) P.C.Silva, 1996 accepted as Aphanocapsa concharum Hansgirg, 1890
57. Species Microcystis delicatissima (W. & G.S.West) Starmach, 1966 accepted as Aphanocapsa delicatissima West & G.S.West, 1912
58. Species Microcystis elabens (Brébisson) Kützing, 1846 accepted as Aphanothece elabens (Meneghini) Elenkin, 1936 (synonym)
59. Species Microcystis elachista (West & G.S.West) Starmach, 1966 accepted as Aphanocapsa elachista West & G.S.West, 1894 (synonym)
60. Species Microcystis feldmannii (Frémy) Kossinskaja, 1948 accepted as Aphanocapsa feldmannii Frémy, 1933 (synonym)
61. Species Microcystis ferruginea Wawrik, 1963 accepted as Cyanogranis ferruginea (F.Wawrik) Hindák ex Hindák, 2006 (synonym)
62. Species Microcystis grevillei (Berkeley) Elenkin, 1938 accepted as Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865 (Synonym)
63. Species Microcystis halophila B.Martens & Pankow, 1972 accepted as Aphanocapsa litoralis Hansgirg, 1892 (synonym)
64. Species Microcystis holsatica (Lemmermann) Lemmermann, 1907 accepted as Aphanocapsa holsatica (Lemmermann) G.Cronberg & Komárek, 1994 (synonym)
65. Species Microcystis incerta (Lemmermann) Lemmermann, 1903 accepted as Aphanocapsa incerta (Lemmermann) G.Cronberg & Komárek, 1994
66. Species Microcystis litoralis (Hansgirg) Aboal, 1988 accepted as Aphanocapsa litoralis Hansgirg, 1892
67. Species Microcystis litoralis (Hansgirg) Forti, 1907 accepted as Aphanocapsa litoralis Hansgirg, 1892 (synonym)
68. Species Microcystis marina (Hansgirg) P.C.Silva, 1996 accepted as Aphanocapsa marina Hansgirg, 1890 (synonym)
69. Species Microcystis mellea Meneghini, 1842 accepted as Gloeocapsa mellea (Meneghini) Kützing, 1847
70. Species Microcystis microcystiformis (Hindák) Joosten, 2006 accepted as Sphaerocavum microcystiforme (Hindák) Azevedo & Sant' Anna, 2003
71. Species Microcystis microspora Meneghini, 1842 accepted as Aphanothece microspora (Meneghini) Rabenhorst, 1863
72. Species Microcystis minima C. Bernard, 1908 accepted as Coelomoron minimum (C. Bernard) J.Komárková-Legnerová & R.Tavera, 1996 (synonym)
73. Species Microcystis minuta Kylin, 1937 accepted as Aphanocapsa minuta (Kylin) Whitton, 2011
74. Species Microcystis minutissima West, 1912 accepted as Anathece minutissima (West) Komárek, Kastovsky & Jezberová, 2011 (synonym)
75. Species Microcystis montigena Hoffmann, 1986 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919 (synonym)
76. Species Microcystis muscicola (Meneghini) Elenkin, 1938 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919 (synonym)
77. Species Microcystis nigra Meneghini, 1842 accepted as Gloeocapsa nigra (Meneghini) Grunow, 1865
78. Species Microcystis pallida (Kützing) Lemmermann, 1907 accepted as Aphanothece pallida (Kützing) Rabenhorst, 1863
79. Species Microcystis parasitica Kützing, 1843 accepted as Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995 (synonym)
80. Species Microcystis paroliniana Meneghini, 1842 accepted as Gloeocapsa paroliniana (Meneghini) Kützing, 1847
81. Species Microcystis protea J.J.Copeland, 1936 accepted as Aphanocapsa protea (J.J.Copeland) Komárek & Anagnostidis, 1995
82. Species Microcystis pulchra (Kützing) J.Stein, 1976 accepted as Microcystis smithii Komárek & Anagnostidis, 1995 (synonym)
83. Species Microcystis punctata J.Schiller, 1954 accepted as Microcystis scripta (P.Richter) Lemmermann, 1903 (synonym)
84. Species Microcystis raspaigellae (Hauck) Kosinskaja, 1948 accepted as Aphanocapsa raspaigellae (Hauck) Frémy, 1933 (synonym)
85. Species Microcystis reinboldii (Richter) Forti, 1907 accepted as Aphanocapsa reinboldii (Richter) Komárek & Anagnostidis, 1995
86. Species Microcystis richteriana (Hieronymus) P.Silva, 1996 accepted as Aphanocapsa richteriana Hieronymus, 1892
87. Species Microcystis salina (Woronichin) Elenkin, 1938 accepted as Aphanocapsa salina Woronichin [Voronichin], 1929
88. Species Microcystis salinarum (Hansgirg) P.C.Silva, 1996 accepted as Aphanocapsa salinarum Hansgirg, 1887
89. Species Microcystis sanguinea (C.Agardh) Kützing, 1833 accepted as Gloeocapsa sanguinea (C.Agardh) Kützing, 1843
90. Species Microcystis stagnalis (Lemmermann) Lemmermann, 1903 accepted as Aphanocapsa stagnalis (Lemmermann) Belyakova, 2004
91. Species Microcystis stereophysalis Meneghini, 1844 accepted as Tetraspora stereophysalis (Meneghini) Kützing, 1847
92. Species Microcystis testacea (Nägeli ex Kützing) Elenkin, 1938 accepted as Aphanocapsa testacea (Kützing) Nägeli, 1849 (synonym)
93. Species Microcystis thermalis (Brügger) Claus, 1959 accepted as Aphanocapsa thermalis Brügger, 1863 (synonym)
94. Species Microcystis violacea (Corda) Kützing, 1833 accepted as Gloeocapsa cordae Guiry, 2017 (synonym)
95. Species Microcystis atrovirens (Corda) Kützing, 1833 (uncertain, uncertain taxonomic status subjected to verification)
96. Species Microcystis densa Schiller, 1956 (uncertain)
97. Species Microcystis migulae G.De Toni, 1939 (uncertain, uncertain taxonomic status subjected to verification)
98. Species Microcystis roseo-persicinus (Kützing) G.S.West, 1904 (uncertain, uncertain taxonomic status subjected to verification)
99. Species Microcystis rubescens (Brébisson) Meneghini, 1842 (uncertain)

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