| Gomphonema subclavatum var. subclavatum (Grunow) Grunow, 1884 |
| Gomphonema subtile Ehrenb., 1843 |
| Gomphonema sundaense Reichardt, 2005 |
| Gomphonema tenellum Kütz., 1844 |
| Gomphonema tenuissimum Fricke, 1904 |
| Gomphonema tergestinum (Grunow) Fricke, 1902 |
| Gomphonema truncatum Ehrenb., 1832 |
| Gomphonema truncatum var. truncatum Ehrenb., 1832 |
| Gomphonema truncatum var. turgidum (Ehrenb.) R.M. Patrick, 1975 |
| Gomphonema undulatum Hust., 1936 |
| Gomphonema utae Lange-Bert. & Reichardt, 1999 |
| Gomphonema ventricosum W. Greg., 1856 |
| Gomphonema ventricosum var. ventricosum W. Greg., 1856 |
| Gomphonema vibrio Ehrenb., 1843 |
| Gomphonema vibrio var. intricatum (Kütz.) R. Ross, 1986 |
| Gomphonema vibrio var. pulvinatum (Braun ex Rabhorst) R.Ross, 1986 |
| Gomphonema vibrioides Reichardt & Lange-Bert., 1991 |
| Gomphonema vitreum Grunow, 1878 |
| Gomphonema wiltschkorum Lange-Bert. apud Lange-Bert. & S.I. Genkal, 1999 |
| Gomphonema yucatanense Metzeltin & Lange-Bert., 1998 |