| Gomphonema parvulum (Kütz.) Kütz., 1849 |
| Gomphonema parvulum var. genuinum A. Mayer, 1919 |
| Gomphonema parvulum var. parvulum (Kütz.) Kütz., 1849 |
| Gomphonema productum (Grunow) Lange-Bert. & Reichardt, 1993 |
| Gomphonema pseudoaugur Lange-Bert., 1979 |
| Gomphonema pseudobohemicum Lange-Bert. & Reichardt, 1996 |
| Gomphonema pseudosphaerophorum H. Kobayasi, 1988 |
| Gomphonema pumilum (Grunow) Reichardt & Lange-Bert., 1991 |
| Gomphonema pumilum var. rigidum Reichardt & Lange-Bert., 1997 |
| Gomphonema pusillum (Grunow, 1880) Kulikovskiy & Kociolek, 2018 |
| Gomphonema pygmaeum Kociolek & Stoermer, 1991 |
| Gomphonema salae Lange-Bert. & Reichardt, 1998 |
| Gomphonema saprophilum (Lange-Bert. & Reichardt) Abraca, R. Jahn, Zimmermann & Enke, 2014 |
| Gomphonema sarcophagus Gregory, 1856 |
| Gomphonema simum M.H. Hohn & J.Hellerman, 1963 |
| Gomphonema sphaerophorum Ehrenb., 1845 |
| Gomphonema stonei E. Reichardt, 1999 |
| Gomphonema subclavatum (Grunow) Grunow, 1884 |
| Gomphonema subclavatum var. commutatum (Grunow) Ant. Mayer, 1919 |
| Gomphonema subclavatum var. mexicanum Grunow (Patrick), 1961 |