1. Species Calothrix aeruginea Thuret ex Bornet & Flahault, 1886
2. Species Calothrix aestuarii Gayral & Mazancourt, 1958
3. Species Calothrix candelii González Guerrero, 1930
4. Species Calothrix chrysaloidea G.S.An, 1989
5. Species Calothrix codicola Setchell & N.L.Gardner, 1930
6. Species Calothrix confervicola C.Agardh ex Bornet & Flahault, 1886
7. Species Calothrix consociata Bornet & Flahault, 1886
8. Species Calothrix contarenii Bornet & Flahault, 1886
9. Species Calothrix cottonii J.De Toni, 1934
10. Species Calothrix cystoseirae Schiffner, 1933
11. Species Calothrix fasciculata C.Agardh ex Bornet & Flahault, 1886
12. Species Calothrix fuscoviolacea P.Crouan & H.Crouan ex Bornet & Flahault, 1886
13. Species Calothrix inserta Nygaard, 1932
14. Species Calothrix litoralis Anand, 1937
15. Species Calothrix longifila W.R.Taylor, 1928
16. Species Calothrix nidulans Setchell & N.L.Gardner, 1924
17. Species Calothrix nodulosa Setchell & N.L.Gardner, 1924
18. Species Calothrix parasitica Thuret ex Bornet & Flahault, 1886
19. Species Calothrix parva Ercegović, 1925
20. Species Calothrix prolifera Flahault, 1886
21. Species Calothrix pulvinata C.Agardh ex Bornet & Flahault, 1886
22. Species Calothrix rectangularis Setchell & N.L.Gardner, 1918
23. Species Calothrix rhizosoleniae Lemmermann, 1899
24. Species Calothrix robusta Setchell & N.L.Gardner, 1918
25. Species Calothrix rosea W.R.Taylor, 1928
26. Species Calothrix scopulorum C.Agardh ex Bornet & Flahault, 1886
27. Species Calothrix vivipara Harvey ex Bornet & Flahault, 1886
28. Species Calothrix aegagropila Kützing, 1833 accepted as Tolypothrix lanata var. aegagropila Hansgirg, 1892 (synonym)
29. Species Calothrix agardhii P.L.Crouan & H.M.Crouan, 1867 accepted as Leibleinia agardhii (Gomont) Anagnostidis & Komárek, 1988 accepted as Lyngbya agardhii Gomont, 1892 (synonym)
30. Species Calothrix chapmannii Lami & Meslin, 1959 accepted as Calothrix cottonii J.De Toni, 1934
31. Species Calothrix comoides Harvey ex Bornet & Flahault, 1886 accepted as Blennothrix comoides (Gomont) Anagnostidis & Komárek, 1988 (synonym)
32. Species Calothrix crustacea Thuret ex Bornet & Flahault, 1886 accepted as Scytonematopsis crustacea (Thuret ex Bornet & Flahault) Koválik & Komárek, 1988
33. Species Calothrix dura Harvey ex Bornet & Flahault, 1886 accepted as Tildenia dura (Harvey ex Bornet & Flahault) Poljanskij, 1936
34. Species Calothrix endophytica A.D.Cotton, 1912 accepted as Calothrix cottonii J.De Toni, 1934
35. Species Calothrix hydnoides Harvey, 1833 accepted as Symploca hydnoides Kützing ex Gomont, 1892 (synonym)
36. Species Calothrix luteofusca C.Agardh, 1827 accepted as Lyngbya luteofusca Gomont, 1892 (synonym)
37. Species Calothrix pilosa Harvey ex Bornet & Flahault, 1886 accepted as Scytonematopsis pilosa (Harvey ex Bornet & Flahault) I.Umezaki & M.Watanabe, 1994 (synonym)
38. Species Calothrix rubra Flahault, 1886 accepted as Homoeothrix rubra P.Crouan & H.Crouan ex Kirchner, 1898 (synonym)
39. Species Calothrix semiplena C.Agardh, 1827 accepted as Lyngbya semiplena J.Agardh ex Gomont, 1892 (synonym)
40. Species Calothrix sordida Zanardini ex Kützing, 1849 accepted as Lyngbya sordida Gomont, 1892 (synonym)
41. Species Calothrix caulerpae Zanardini, 1851 (uncertain)
42. Species Calothrix elongata Zanardini, 1943 (uncertain, uncertain taxonomic status subjected to verification)
43. Species Calothrix evoluta Y.Y.Li, 1989 (uncertain, uncertain taxonomic status subjected to verification)
44. Species Calothrix infestans Harvey ex Forti, 1907 (uncertain, uncertain taxonomic status subjected to verification)
45. Species Calothrix nemalii Zanardini, 1843 (uncertain, uncertain taxonomic status subjected to verification)
46. Species Calothrix pannosa C.Agardh, 1827 (uncertain)
47. Species Calothrix stellulata Zanardini, 1840 (uncertain)
48. Species Calothrix variegata Zanardini, 1840 (uncertain)
49. Species Calothrix violacea Zanardini, 1843 (uncertain, uncertain taxonomic status subjected to verification)

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