1. Species Aphanocapsa albida Zeller, 1873
2. Species Aphanocapsa annulata G.B.McGregor, 2007
3. Species Aphanocapsa arctica Whelden, 1947
4. Species Aphanocapsa banaresensis Bharadwaja, 1935
5. Species Aphanocapsa benaresensis Bharadwaja, 1935
6. Species Aphanocapsa biformis A.Braun, 1879
7. Species Aphanocapsa botryoides J.J.Copeland, 1936
8. Species Aphanocapsa brunnea (A.Baun ex Kützing) Nägeli, 1849
9. Species Aphanocapsa concharum Hansgirg, 1890
10. Species Aphanocapsa conferta (West & G.S.West) Komárková-Legnerová & Cronberg, 1994
11. Species Aphanocapsa crassa Ghose, 1927
12. Species Aphanocapsa cumulus Komárek & Cronberg, 1999
13. Species Aphanocapsa delicatissima West & G.S.West, 1912
14. Species Aphanocapsa depressa (Berkeley) Rabenhorst, 1865
15. Species Aphanocapsa dharwadensis Bongale, 1987
16. Species Aphanocapsa distans Zalessky, 1926
17. Species Aphanocapsa elachista West & G.S.West, 1894
18. Species Aphanocapsa elegans (Lemmermann) Joosten, 2006
19. Species Aphanocapsa farlowiana Drouet & Daily, 1942
20. Species Aphanocapsa feldmannii Frémy, 1933
21. Species Aphanocapsa ferruginea Beck-Mannagetta, 1931
22. Species Aphanocapsa florae Lami, 1936
23. Species Aphanocapsa fonticola Hansgirg, 1890
24. Species Aphanocapsa fuscolutea Hansgirg, 1893
25. Species Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865
26. Species Aphanocapsa holsatica (Lemmermann) G.Cronberg & Komárek, 1994
27. Species Aphanocapsa howei Collins, 1920
28. Species Aphanocapsa hyalina (Lyngbye) Hansgirg, 1893
29. Species Aphanocapsa incerta (Lemmermann) G.Cronberg & Komárek, 1994
30. Species Aphanocapsa intertexta N.L.Gardner, 1927
31. Species Aphanocapsa koordersii K.Strøm, 1923
32. Species Aphanocapsa kovacekii Belyakova, 2004
33. Species Aphanocapsa le-jolisii (Thuret) Frémy, 1924
34. Species Aphanocapsa lewisii A.M.Keefe, 1927
35. Species Aphanocapsa lilacina Miscoe & J.R.Johansen, 2016
36. Species Aphanocapsa litoralis Hansgirg, 1892
37. Species Aphanocapsa marina Hansgirg, 1890
38. Species Aphanocapsa minuta (Kylin) Whitton, 2011
39. Species Aphanocapsa muscicola (Meneghini) Wille, 1919
40. Species Aphanocapsa nivalis Lagerheim, 1894
41. Species Aphanocapsa nubila Komárek & H.J.Kling, 1991
42. Species Aphanocapsa paludosa Rabenhorst, 1863
43. Species Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995
44. Species Aphanocapsa parietina Nägeli, 1849
45. Species Aphanocapsa planctonica (G.M.Smith) Komárek & Anagnostidis, 1995
46. Species Aphanocapsa protea (J.J.Copeland) Komárek & Anagnostidis, 1995
47. Species Aphanocapsa raspaigellae (Hauck) Frémy, 1933
48. Species Aphanocapsa reinboldii (Richter) Komárek & Anagnostidis, 1995
49. Species Aphanocapsa richteriana Hieronymus, 1892
50. Species Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865
51. Species Aphanocapsa roberti-lamii Frémy, 1934
52. Species Aphanocapsa roeseana De Bary, 1870
53. Species Aphanocapsa salina Woronichin [Voronichin], 1929
54. Species Aphanocapsa salinarum Hansgirg, 1887
55. Species Aphanocapsa sideroderma Naumann, 1922
56. Species Aphanocapsa stagnalis (Lemmermann) Beljakova, 2004
57. Species Aphanocapsa testacea (Kützing) Nägeli, 1849
58. Species Aphanocapsa thermalis Brügger, 1863
59. Species Aphanocapsa tolliana J.J.Copeland, 1936
60. Species Aphanocapsa venezuelae Schiller, 1956
61. Species Aphanocapsa violacea Grunow, 1865
62. Species Aphanocapsa zanardinii (Hauck) Hansgirg, 1889
63. Species Aphanocapsa anodontae Hansgirg, 1893 accepted as Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865 (synonym)
64. Species Aphanocapsa aurantia (C.Agardh) Rabenhorst, 1865 accepted as Chroococcus aurantius (C.Agardh) Wille, 1918
65. Species Aphanocapsa castagnei (Kützing) Rabenhorst, 1865 accepted as Aphanothece castagnei (Kützing) Rabenhorst, 1865
66. Species Aphanocapsa cruenta (Smith) Hansgirg, 1885 accepted as Porphyridium purpureum (Bory) K.M.Drew & R.Ross, 1965 (synonym)
67. Species Aphanocapsa endolithica Ercegović, 1925 accepted as Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865
68. Species Aphanocapsa endophytica G.M.Smith, 1920 accepted as Synechocystis endobiotica (Elenkin & Hollerbach) Elenkin, 1938 (synonym)
69. Species Aphanocapsa membranacea Rabenhorst, 1865 accepted as Gloeothece membranacea (Rabenhorst) Bornet, 1892
70. Species Aphanocapsa minima Migula, 1933 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919 (synonym)
71. Species Aphanocapsa montana C.E.Cramer, 1862 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919 (synonym)
72. Species Aphanocapsa naegelii P.Richter, 1884 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919 (synonym)
73. Species Aphanocapsa orae (Kossinskaja) Komárek & Anagnostidis, 1995 accepted as Aphanocapsa litoralis Hansgirg, 1892
74. Species Aphanocapsa pulchra (Kützing) Rabenhorst, 1865 accepted as Microcystis smithii Komárek & Anagnostidis, 1995 (Synonym)
75. Species Aphanocapsa pulvera (H.C.Wood) Kovalik accepted as Microcystis pulverea (H.C.Wood) Forti, 1907
76. Species Aphanocapsa roseana De Bary, 1870 accepted as Aphanocapsa roeseana De Bary, 1870
77. Species Aphanocapsa siderosphaera Naumann, 1922 accepted as Aphanocapsa sideroderma Naumann, 1922 (synonym)
78. Species Aphanocapsa smaragdina (Hauck) Hansgirg, 1889 accepted as Chroococcus smaragdinus Hauck, 1888
79. Species Aphanocapsa virescens (Hassall) Rabenhorst, 1865 accepted as Aphanocapsa parietina Nägeli, 1849 (synonym)
80. Species Aphanocapsa wittrockii (Richter) Hansgirg, 1885 accepted as Porphyridium wittrockii Richter, 1882 (synonym)
81. Species Aphanocapsa fremyi Belyakova, 2000 (uncertain)
82. Species Aphanocapsa hardesii Schiller (uncertain)
83. Species Aphanocapsa nebulosa A.Braun, 1876 (uncertain)
84. Species Aphanocapsa rufescens Hansgirg, 1892 (uncertain)
85. Species Aphanocapsa sesciacensis Frémy, 1928 (uncertain)

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