• Aphanocapsa Nägeli, 1849
• Aphanocapsa albida Zeller, 1873
• Aphanocapsa annulata G.B. McGregor
• Aphanocapsa anodontae Hansgirg, 1892 accepted as Aphanocapsa rivularis (Carmicheal) Rabenhorst, 1865
• Aphanocapsa arctica Whelden, 1947
• Aphanocapsa aurantia (C. Agardh) Rabenhorst
• Aphanocapsa banaresensis Bharadvaja, 1935
• Aphanocapsa benaresensis Bharadwaja, 1935
• Aphanocapsa biformis A. Braun, 1876
• Aphanocapsa botryoides Copeland, 1936
• Aphanocapsa brunnea (A. Baun) Nägeli, 1849
• Aphanocapsa castagnei (Kützing) Rabenhorst
• Aphanocapsa concharum Hansgirg, 1890 accepted as Microcystis concharum (Hansgirg) P. Silva, 1996
• Aphanocapsa conferta (W. West & G.S. West) Komárková-Legnerová & Cronberg, 1993
• Aphanocapsa crassa Ghose, 1927
• Aphanocapsa cumulus Komárek & Cronberg, 1999
• Aphanocapsa delicatissima W. West & G.S. West, 1912
• Aphanocapsa depressa (Berkeley) Rabenhorst, 1865
• Aphanocapsa distans Zalessky, 1926
• Aphanocapsa elachista W. West & G.S. West, 1894 accepted as Microcystis elachista (W. West & G.S. West) Compère, 1967
• Aphanocapsa endolithica Ercegovic, 1925 accepted as Aphanocapsa rivularis (Carmicheal) Rabenhorst, 1865
• Aphanocapsa endophytica G.M. Smith, 1920 accepted as Synechocystis endobiotica (Elenkin & Hollerbach) Elenkin, 1938
• Aphanocapsa farlowiana Drouet & Daily, 1942
• Aphanocapsa feldmannii Frémy, 1933
• Aphanocapsa ferruginea Beck-Mannagetta, 1931
• Aphanocapsa flava (Kützing) Rabenhorst, 1865 accepted as Aphanocapsa parietina Nägeli, 1849
• Aphanocapsa florae Lami
• Aphanocapsa fonticola Hansgirg, 1890
• Aphanocapsa fuscolutea Hansgirg, 1892
• Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865 accepted as Aphanocapsa grevillei (Hassall) Rabenhorst, 1865
• Aphanocapsa grevillei (Hassall) Rabenhorst, 1865
• Aphanocapsa hardesii Schiller
• Aphanocapsa holsatica (Lemmermann) G. Cronberg & J. Komárek, 1994
• Aphanocapsa howei Collins, 1920
• Aphanocapsa hyalina (Lyngbye) Hansgirg, 1892
• Aphanocapsa incerta (Lemmermann) Cronberg & Komárek, 1994
• Aphanocapsa intertexta Gardner, 1927
• Aphanocapsa koordersii K. Strøm, 1923
• Aphanocapsa le-jolisii (Thuret) Frémy, 1924
• Aphanocapsa lewisii Keefe, 1927
• Aphanocapsa litoralis (Hansgirg) Komárek & Anagnostidis, 1995
• Aphanocapsa litoralis Hansgirg, 1892
• Aphanocapsa marina Hansgirg, 1890 accepted as Microcystis marina (Hansgirg) P.C. Silva, 1996
• Aphanocapsa membranacea Rabenhorst
• Aphanocapsa minima Migula, 1933 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919
• Aphanocapsa montana Cramer, 1862 accepted as Microcystis richteriana (Hieronymus) P. Silva, 1996
• Aphanocapsa muscicola (Meneghini) Wille, 1919
• Aphanocapsa naegelii Richter, 1884 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919
• Aphanocapsa nebulosa A. Braun
• Aphanocapsa nivalis Lagerheim, 1894
• Aphanocapsa nubila J. Komárek & H.J. Kling, 1991
• Aphanocapsa orae (Kosinskaja) Komárek & Anagnostidis, 1995
• Aphanocapsa pallida Rabenhorst
• Aphanocapsa paludosa Rabenhorst
• Aphanocapsa parallelliformis Cronberg
• Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995
• Aphanocapsa parietina Nägeli, 1849
• Aphanocapsa planctonica (G.M. Smith) Komárek & Anagnostidis, 1995
• Aphanocapsa protea (Copeland) Komárek & Anagnostidis, 1995
• Aphanocapsa pulchra (Kützing) Rabenhorst, 1865 accepted as Microcystis smithii Komárek & Anagnostidis, 1995
• Aphanocapsa pusilla Vogel
• Aphanocapsa raspaigellae (Hauck) Frémy, 1933
• Aphanocapsa reinboldii (Richter) Komárek & Anagnostidis, 1995
• Aphanocapsa richteriana Hieronymus, 1892 accepted as Microcystis richteriana (Hieronymus) P. Silva, 1996
• Aphanocapsa rivularis (Carmicheal) Rabenhorst, 1865
• Aphanocapsa robertilamii Frémy, 1934
• Aphanocapsa roeseana De Bary, 1870
• Aphanocapsa roseana De Bary
• Aphanocapsa rufescens Hansgirg, 1892
• Aphanocapsa salina Woronichin, 1929 accepted as Microcystis salina (Woronichin) Elenkin, 1938
• Aphanocapsa salinarum Hansgirg, 1887 accepted as Microcystis salinarum (Hansgirg) P. Silva, 1996
• Aphanocapsa sesciacensis Frémy, 1928
• Aphanocapsa sideroderma Naumann, 1922
• Aphanocapsa siderosphaera Naumann, 1922 accepted as Aphanocapsa sideroderma Naumann, 1922
• Aphanocapsa smaragdina (Hauck) Hansgirg, 1889
• Aphanocapsa testacea Nägeli, 1949
• Aphanocapsa thermalis Brügger, 1863
• Aphanocapsa tolliana Copeland, 1936
• Aphanocapsa venezuelae Schiller, 1952
• Aphanocapsa violacea Grunow, 1865
• Aphanocapsa virescens (Hassall) Rabenhorst, 1865 accepted as Aphanocapsa parietina Nägeli, 1849
• Aphanocapsa zanardinii (Hauck) Hansgirg, 1889
• Aphanocapsaopsis P.K. Maithy & M. Shukla, 1977 †
• Aphanocapsaopsis ramapuraensis P.K. Maithy & M. Shukla †
• Aphanocapsaopsis sitholeyi P.K. Maithy & M. Shukla †