| Gomphonema grunowii Patrick, 1975 |
| Gomphonema helveticum Brun, 1895 |
| Gomphonema intricatum Kütz., 1844 |
| Gomphonema intricatum var. intricatum Kütz., 1844 |
| Gomphonema intricatum var. vibrio (Ehrenb.) Cleve, 1894 |
| Gomphonema lanceolatum Agardh, 1831 |
| Gomphonema longiceps Ehrenb., 1845 |
| Gomphonema mexicanum Grunow, 1880 |
| Gomphonema minutum (C. Agardh) C. Agardh, 1831 |
| Gomphonema olivaceum (Hornemann) Bréb., 1838 |
| Gomphonema parvulum (Kütz.) Kütz., 1849 |
| Gomphonema parvulum var. genuinum A. Mayer, 1919 |
| Gomphonema parvulum var. parvulum (Kütz.) Kütz., 1849 |
| Gomphonema pseudoaugur Lange-Bert., 1979 |
| Gomphonema subclavatum (Grunow) Grunow, 1884 |
| Gomphonema subclavatum var. commutatum (Grunow) Ant. Mayer, 1919 |
| Gomphonema subclavatum var. mexicanum Grunow (Patrick), 1961 |
| Gomphonema subclavatum var. subclavatum (Grunow) Grunow, 1884 |
| Gomphonema tergestinum (Grunow) Fricke, 1902 |
| Gomphonema truncatum Ehrenb., 1832 |