| Gomphonema lanceolatum Agardh, 1831 |
| Gomphonema laticollum Reichardt, 2001 |
| Gomphonema lepidum Fricke, 1904 |
| Gomphonema lippertii E. Reichardt & Lange-Bert. apud E. Reichardt, 1999 |
| Gomphonema longiceps Ehrenb., 1845 |
| Gomphonema maclaughlinii E. Reichardt, 1999 |
| Gomphonema mariovense Levkov & Tofilovska, 2016 |
| Gomphonema martini Fricke, 1902 |
| Gomphonema meridionale Kociolek & E.W.Thomas, 2009 |
| Gomphonema mexicanum Grunow, 1880 |
| Gomphonema micropus Kütz., 1844 |
| Gomphonema minusculum Krasske, 1932 |
| Gomphonema minutum (C. Agardh) C. Agardh, 1831 |
| Gomphonema minutum f. pachypus Lange-Bert. & E. Reichardt, 1993 |
| Gomphonema minutum f. syriacum Lange-Bert. & Reichardt, 1991 |
| Gomphonema naviculoides W. Sm., 1856 |
| Gomphonema novacula M.H. Hohn & J.Hellerman, 1963 |
| Gomphonema olivaceum (Hornemann) Bréb., 1838 |
| Gomphonema parvuliforme Levkov, Mitic-Kopanja & Reichardt, 2016 |
| Gomphonema parvulius (Lange-Bert. & Reichardt) Lange-Bert. & Reichardt, 1996 |