Cyclostephanos dubius can be distinguished from Stephanodiscus alpinus and S. agassizensis by its more coarse structure and characteristic alveoli near the valve margin. In North America, the absence of spines in C. dubius also differentiates it from most Stephanodiscus species. Very small specimens of C. dubius might be confused with S. minutulus, but S. minutulus has distinct spines visible in the light microscope, even in small specimens.