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 than G. kobayasii.
Reichardt and Lange-Bertalot (Reichardt 1997) proposed the new taxon G. pumilum var. rigidum, whose length and breadth measurements are very similar to G. kobayasii and both are similar to other “typical” Gomphonema species by having occluded areolae. The European variety differs from G. kobayasii by the shape of the valves (more asymmetric about the transapical axis) and having finer striae (11-14 in 10 µm versus 9-12 in 10 µm). Reichardt (1997) illustrated specimens from the US, but they are interpreted here as G. kobayasii, differing from the European specimens in shape. Further research on the G. pumilum group sensu lato is necessary to more finely determine species boundaries.