| Gomphonema dichotomum var. affine (Kütz.) Rabenh., 1864 |
| Gomphonema dichotomum var. dichotomun Kütz., 1833 |
| Gomphonema dubravicense Pantocsek, 1892 |
| Gomphonema entolejum Østrup, 1902 |
| Gomphonema exilissimum (Grunow) Lange-Bert. & Reichardt, 1996 |
| Gomphonema gandhii B. Karthick & Kociolek, 2011 |
| Gomphonema gracile Ehrenb., 1838 |
| Gomphonema graciledictum Reichardt, 2015 |
| Gomphonema grovei M. Schmidt, 1899 |
| Gomphonema grunowii Patrick, 1975 |
| Gomphonema hebridense W. Gregory, 1854 |
| Gomphonema helveticum Brun, 1895 |
| Gomphonema innocens Reichardt, 1999 |
| Gomphonema insigne Gregory, 1856 |
| Gomphonema intricatum Kütz., 1844 |
| Gomphonema intricatum var. intricatum Kütz., 1844 |
| Gomphonema intricatum var. vibrio (Ehrenb.) Cleve, 1894 |
| Gomphonema kobayashiae Metzeltin & Lange-Bert., 1998 |
| Gomphonema kobayasii Kociolek & J.C.Kingston, 1999 |
| Gomphonema lagenula Kütz., 1844 |