Gomphoneis exigua (Kützing) Medlin
Gomphoneis olivacea (Lyngbye) P.A.Dawson, 1974 accepted as Gomphonema olivaceum (Lyngbye) Desmazières, 1825
Gomphonema acuminatum Ehrenberg, 1832
Gomphonema acuminatum sensu Grunow in Van Heurck, 1880 (uncertain > unassessed )
Gomphonema acuminatum var. coronatum (Ehrenberg) Ehrenberg, 1864 accepted as Gomphonema coronatum Ehrenberg, 1840
Gomphonema affine Kützing, 1844
Gomphonema affine var. kerguelenense (Manguin) Germain & Le Cohu, 1981 (uncertain > unassessed )
Gomphonema angustatum (Kützing) Rabenhorst, 1864 (uncertain > unassessed )
Gomphonema angustatum sensu Brebisson (uncertain > unassessed )
Gomphonema coronatum Ehrenberg, 1840 (uncertain > unassessed )
Gomphonema exiguum (Ostrup) Fricke, 1902 (uncertain > unassessed )
Gomphonema exiguum Kützing, 1844 accepted as Gomphoneis exigua (Kützing) Medlin
Gomphonema gracile Ehrenberg, 1838 (uncertain > unassessed )
Gomphonema intricatum Kützing, 1844
Gomphonema kamtschaticum Grunow, 1878 accepted as Pseudogomphonema kamtschaticum (Grunow) L.K.Medlin, 1986 accepted as Gomphonema kamtschaticum var. kamtschaticum Grunow, 1878
Gomphonema kamtschaticum var. kamtschaticum Grunow, 1878 (uncertain > unassessed )
Gomphonema kerguelenensis E.E.Manguin, 1954
Gomphonema olivaceum (Hornemann) Brébisson, 1838 (uncertain > unassessed )
Gomphonema olivaceum (Hornemann) Ehrenberg, 1838 (uncertain > unassessed )
Gomphonema olivaceum (Lyngbye) Desmazières, 1825
Gomphonema olivaceum var. tenellum (Kützing) Cleve, 1894 accepted as Gomphonema tenellum var. tenellum Kützing, 1844
Gomphonema parvulum (Kützing) Kützing, 1849
Gomphonema parvulum var. subelliptica Cleve, 1894 (uncertain > unassessed )
Gomphonema productum (Grunow) Lange-Bertalot & Reichardt, 1993 (uncertain > unassessed )
Gomphonema signyensis Kociolek & Jones, 1995 (uncertain > unassessed )
Gomphonema tenellum sensu Grunow in Van Heurck, 1880 (uncertain > unassessed )
Gomphonema tenellum var. tenellum Kützing, 1844 (uncertain > unassessed )
Gomphonema vitreum Grunow, 1878 (uncertain > unassessed )