| Gomphonema apuncto Wallace, 1960 |
| Gomphonema aquaemineralis Lange-Bert. & Reichardt, 1991 |
| Gomphonema astridiae Lange-Bert. & S.I. Genkal, 1999 |
| Gomphonema augur Ehrenb., 1841 |
| Gomphonema auritum A. Braun ex Kütz., 1849 |
| Gomphonema bourbonense Reichardt, 1997 |
| Gomphonema brasiliense Grunow, 1878 |
| Gomphonema brasiliense var. brasiliense Grunow, 1878 |
| Gomphonema brasiliensoides Metzeltin, Lange-Bert. & García-Rodríguez, 2005 |
| Gomphonema capitatum Ehrenb., 1838 |
| Gomphonema carolinense Hagelstein, 1939 |
| Gomphonema catena (Ehrenb.) Rabenhorst, 1864 |
| Gomphonema clavatum Ehrenb., 1832 |
| Gomphonema clevei Fricke, 1902 |
| Gomphonema clevei var. javanica Hust., 1937 |
| Gomphonema commutatum Grunow, 1880 |
| Gomphonema coronatum Ehrenb., 1841 |
| Gomphonema cumrhis M.H. Hohn & J.Hellerman, 1963 |
| Gomphonema curvatum Kütz., 1833 |
| Gomphonema dichotomum Kütz., 1833 |