Cocconeis antiqua J.A.Tempère & J.-J.Brun, 1889 †
Cocconeis costata Gregory, 1855
Cocconeis costata var. antarctica Manguin, 1960 (uncertain > unassessed )
Cocconeis costata var. pacifica (Grunow) Cleve, 1895 (uncertain > unassessed )
Cocconeis euglypta Ehrenberg, 1854 (uncertain > unassessed )
Cocconeis fasciolata (Ehrenberg) N.E.Brown, 1920 accepted as Rhaphoneis fasciolata var. fasciolata Ehrenberg, 1844
Cocconeis imperatrix A.W.F.Schmidt, 1894 accepted as Cocconeis fasciolata (Ehrenberg) N.E.Brown, 1920 accepted as Rhaphoneis fasciolata var. fasciolata Ehrenberg, 1844
Cocconeis infirmata Manguin, 1957 (uncertain > unassessed )
Cocconeis lineata Ehrenberg, 1843 (uncertain > unassessed )
Cocconeis litigiosa van Heurck, 1909 (uncertain > unassessed )
Cocconeis pinnata W.Gregory ex Greville, 1859
Cocconeis placentula (Skvortzow) Skabichevskii, 1977 (uncertain > unassessed )
Cocconeis placentula Ehrenberg, 1838
Cocconeis placentula var. euglypta (Ehrenberg) Grunow, 1884 accepted as Cocconeis euglypta Ehrenberg, 1854
Cocconeis placentula var. lineata (Ehrenberg) van Heurck, 1885 accepted as Cocconeis lineata Ehrenberg, 1843
Cocconeis placentula var. trilineata (M. Peragallo & Héribaud in Héribaud) Cleve, 1895 accepted as Cocconeis trilineatus M. Peragallo & Héribaud in Héribaud, 1893
Cocconeis schuetii (uncertain > unassessed )
Cocconeis schuettii van Heurck, 1909 accepted as Cocconeis antiqua J.A.Tempère & J.-J.Brun, 1889 †
Cocconeis scutellum Ehrenberg, 1838
Cocconeis scutellum Meunier, 1910 (uncertain > unassessed )
Cocconeis scutellum f. parva Grunow, 1880 (uncertain > unassessed )
Cocconeis scutellum var. parva (Grunow) Cleve, 1895 accepted as Cocconeis scutellum f. parva Grunow, 1880
Cocconeis therezieni LeCohu & Maillard, 1983 (uncertain > unassessed )
Cocconeis trilineatus M. Peragallo & Héribaud in Héribaud, 1893 (uncertain > unassessed )
Cocconeis wienckensis Petit, 1908 (uncertain > unassessed )