Gomphonema insularum is similar in length, breadth, and stria density but has a less linear, more lanceolate, even slightly clavate outline. Gomphonema insularum also has more uniformly short striae throughout the valve and round depressions on external valve surface.
Gomphonema incognitum is considerably more clavate. Gomphonema christenseni is both larger and lacks an isolated stigmoid.
Gomphonema freesei has a greater length and width.