Gomphonema variostriatum has a distinctly asymmetric central area, and striae density varies greatly between central valve and apices. This species has been confused with G. minutum and G. bavaricum. Valves of G. kobayasii are more lanceolate than G. minutum and have a wider central area. Gomphonema minutum has doubly-punctate striae, while G. kobayasii has striae composed of single rows of areolae.
Gomphonema bavaricum is longer and wider.