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.