Stephanodiscus niagarae can be distinguished from S. reimeri by the areola density; 11-20 vs 8-12 in 10 µm, respectively. These two species can also be distinguished by the size and shape of the areolae. While S. niagarae has small, round areolae, S. reimeri has unusually shaped trapezoidal to sub-hexagonal areolae. Stephanodiscus alpinus has comparatively large, hyaline interfascicles (costae), each with a spine at the valve face margin. In contrast, S. reimeri has a marginal spine at the end of every 2-3 costae. Compared to S. reimeri, S. superiorensis is smaller (39-72 µm), only slightly arched in the valve center, and has spines on every third or fourth costa.