Gomphonema caperatum has shorter, more narrow valves, and a more broadly lanceolate axial area.
Gomphonema christenseni lacks a stigmoid and the headpole end is more tapered.
Gomphonema incognitum is smaller in both length and width.
Gomphonema insularum has shorter, more narrow valves, a more broadly lanceolate axial area that does not expand into a defined central area and a sinuous raphe.
Gomphonema stoermeri has shorter, more narrow valves, a narrower axial area, and a smaller central area.
Gomphonema amerhombicum has more finely spaced striae (>14 in 10 µm) and the footpole has somewhat concave margins.