1. Species Synechococcus ambiguus Skuja, 1937
2. Species Synechococcus arcuatus J.J.Copeland, 1936
3. Species Synechococcus bosshardii Skuja, 1932
4. Species Synechococcus brunneolus Rabenhorst, 1863
5. Species Synechococcus capitatus A.E.Bailey-Watts & Komárek, 1991
6. Species Synechococcus carcerarius R.E.Norris, 1967
7. Species Synechococcus elongatus (Nägeli) Nägeli, 1849
8. Species Synechococcus endogloeicus Hindák, 1996
9. Species Synechococcus epigloeicus Hindák, 1996
10. Species Synechococcus euryphyes Beck-Mannagetta [Beck von Mannagetta], 1927
11. Species Synechococcus ferrunginosus Wawrik, 1979
12. Species Synechococcus intermedius N.L.Gardner, 1927
13. Species Synechococcus koidzumii Yoneda, 1943
14. Species Synechococcus lividus J.J.Copeland, 1936
15. Species Synechococcus marinus C.-C.Jao, 1948
16. Species Synechococcus moorigangae Singh & Bhadury, 2019
17. Species Synechococcus mucicolus Joosten, 2006
18. Species Synechococcus mundulus Skuja, 1964
19. Species Synechococcus nidulans (Pringsheim) Komárek, 1970
20. Species Synechococcus rhodobaktron Komárek & Anagnostidis, 1995
21. Species Synechococcus roseopurpureus G.S.West, 1899
22. Species Synechococcus salinarum Komárek, 1956
23. Species Synechococcus sciophilus Skuja, 1964
24. Species Synechococcus sigmoideus (G.T.Moore & N.Carter) Komárek, 1970
25. Species Synechococcus sublividus Emoto & Yoneda, 1941
26. Species Synechococcus subsalsus Skuja, 1939
27. Species Synechococcus sulphuricus Dor, 1967
28. Species Synechococcus vantieghemii (Pringsheim) Bourrelly, 1970
29. Species Synechococcus violaceus Grunow, 1868
30. Species Synechococcus vulcanus J.J.Copeland, 1936
31. Species Synechococcus aeruginosus Nägeli, 1849 accepted as Cyanothece aeruginosa (Nägeli) Komárek, 1976
32. Species Synechococcus amethystinus J.J.Copeland, 1936 accepted as Cyanobium amethystinum (J.J.Copeland) J.Komárek, J.Kopecký & V.Cepák, 1999
33. Species Synechococcus bacillaris Butcher, 1952 accepted as Cyanobium bacillare (Butcher) Komárek, Kopeck & Cepák, 1999 (synonym)
34. Species Synechococcus bigranulatus Skuja, 1933 accepted as Thermostichus bigranulatus (Skuja) Komárek & Strunecky, 2020
35. Species Synechococcus cedrorum Sauvageau, 1892 accepted as Cyanobacterium cedrorum (Sauvageau) Komárek, J.Kopecký & Cepák, 1999 (synonym)
36. Species Synechococcus chlorinus (Böcher) Komárek, 1970 accepted as Romeria chlorinaBoecher Böcher, 1949
37. Species Synechococcus diachloros Skuja, 1939 accepted as Cyanobacterium diachloros (Skuja) Komárek, Kopecký & Cepák, 1990 (synonym)
38. Species Synechococcus diatomicola Geitler, 1953 accepted as Cyanobium diatomicola (Geitler) Komárek, Kopecký & Cepák, 1999 (synonym)
39. Species Synechococcus elegans (Woloszynska) Komárek, 1970 accepted as Romeria elegans (Woloszynska) Geitler, 1932
40. Species Synechococcus endophyticus (West & G.S.West) Joosten, 2006 accepted as Anathece endophytica (W. & G.S. West) Komárek, Kastovsky & Jezberová, 2011
41. Species Synechococcus eximius J.J.Copeland, 1936 accepted as Cyanobium eximium (J.J.Copeland) Komárek, Kopecký & Cepák, 1999
42. Species Synechococcus gaarderi Ålvik, 1934 accepted as Cyanobium gaarderi (Ålvik) Komárek, Kopecký & Cepák, 1999 (synonym)
43. Species Synechococcus geitleri De Toni, 1936 accepted as Synechococcus elongatus (Nägeli) Nägeli, 1849 (synonym)
44. Species Synechococcus gracilis (Koczwara) Komárek, 1970 accepted as Romeria gracilis (Koczwara) Koczwara, 1932
45. Species Synechococcus leopoliensis (Raciborski) Komárek, 1970 accepted as Romeria leopoliensis (Raciborski) Koczwara, 1932
46. Species Synechococcus linearis (Schmidle & Lauterborn) Komárek, 1970 accepted as Rhabdoderma lineare Schmidle & Lauterborn, 1900 (synonym)
47. Species Synechococcus major J.Schröter, 1884 accepted as Cyanothece major (Schröter) Komárek, 1976 (synonym)
48. Species Synechococcus marinus Ercegovic, 1932 accepted as Aphanothece marina (Ercegovic) Komárek & Anagnostidis, 1995 (synonym)
49. Species Synechococcus minervae J.J.Copeland, 1936 accepted as Cyanobacterium minervae (J.J.Copeland) Komárek, Kopecký & Cepák, 1999
50. Species Synechococcus minimus (Lemmermann) Komárek, 1970 accepted as Romeria minima (Lemmermann) Komárek, 2001
51. Species Synechococcus notatus Skuja, 1964 accepted as Cyanobacterium notatum (Skuja) Komárek, Kopecký & Cepák, 1999 (synonym)
52. Species Synechococcus oceanicus W.T.Hall & G.Claus, 1965 accepted as Cyanobium oceanicum (W.T.Hall & G.Claus) Komárek, Kopecký & Cepák, 1999
53. Species Synechococcus parvulus Nägeli, 1948 accepted as Synechococcus elongatus (Nägeli) Nägeli, 1849 (synonym)
54. Species Synechococcus parvus Migula, 1906 accepted as Cyanobium parvum (Migula) Komárek, J.Kopecký & Cepák, 1999 (synonym)
55. Species Synechococcus plancticus G.Drews, H.Prauser & D.Uhlmann, 1961 accepted as Cyanobium plancticum (G.Drews, H.Prauser & D.Uhlmann) Komárek, Kopecký & Cepák, 1999 (synonym)
56. Species Synechococcus praelongus Emoto & Yoneda, 1941 accepted as Thermostichus praelongus (Emoto & Yonedo) Komárek & Strunecky, 2020
57. Species Synechococcus racemosus Wolle, 1881 accepted as Synechococcus elongatus (Nägeli) Nägeli, 1849 (synonym)
58. Species Synechococcus roseus J.J.Copeland, 1936 accepted as Cyanobium roseum (J.J.Copeland) Komárek, Kopecký & Cepák, 1999
59. Species Synechococcus rubescens T.P.Chang, 1980 accepted as Cyanobium rubescens (T.P.Chang) Komárek, Kopeck & Cepák, 1999 (synonym)
60. Species Synechococcus vescus J.J.Copeland, 1936 accepted as Thermostichus vescus (Copeland) Komárek, 2020
61. Species Synechococcus virga-rosea T.P.Chang, 1980 accepted as Cyanobium virga-rosea (T.P.Chang) Komárek, Kopecký & Cepák, 1999 (synonym)
62. Species Synechococcus viridissimus Copeland, 1936 accepted as Thermostichus viridissimus (Copeland) Komárek & Strunecky, 2020
63. Species Synechococcus spongiarum Usher, Toze, Fromont, Kuo & Sutton, 2004 (uncertain)

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