Gomphonema mehleri has a wider headpole and coarsely punctate striae.
Gomphonema submehleri has less radiate striae and a higher stria density at the apices.
Gomphonema manubrium has a wider headpole, wider axial area and the stigmoid is more distant from the striae.
Gomphonema ventricosum has a wider headpole, an irregularly elliptic central area and the stigmoid is more distant from the striae.