The faint markings in the axial and central areas distinguish C.crassipunctata from most other large species of Cymbopleura. Cymbopleura heinii may also have these faint spots but it has higher areolae density in the striae. Cymbella inaequalis is further distinguished by having a straight raphe and rhomboid-lanceolate valves. Cymbopleura heinii, C. subrostrata, and C. neoheteropleura have hooked or crosier-shaped proximal raphe ends.