Gomphonema gracile has more more acute apices and a narrow axial area.
Gomphonema affine has wider valves (7-12 µm).
Gomphonema insigne has wider valves (7.5-13 µm) and coarser striae (6-8 in 10 µm).
Gomphonema submehleri has a more strongly clavate valve outline, wider valves (5.2-7.8 µm), and a higher head pole stria density (14-16 in 10 µm).