Gomphonema intricatum var. pumilum has a protracted headpole, nearly parallel sides, and a narrow axial area with a rectangular central area. Gomphonema tenellum has a more linear valve outline. Gomphonema intricatum var. minor is smaller (12-18 µm in length and 2.5-3.4 µm in width) than var. pumilum. Lack of areolae "crowded", or more dense, at the headpole and presence of external C-shaped flaps separate this taxon from G. intricatum and other members of the group.