Aulacoseira pusilla differs from several Aulacoseira species with low-mantles by having curved pervalvar rows of areolae and a distinct, shelf-like ringleiste. Aulacoseira alpigena has similar frustule proportions, size, mantle rows of areolae and ringleiste to A. pusilla, but differs by having thin spines at the end of each costa. Furthermore, the valves of A. pusilla have thick spines that originate from two or three pervalvar costae. The frustule structure of A. pusilla is similar to that of A. subarctica, but the latter species has a higher mantle, a high ratio of mantle height to valve diameter, and longer spines. Aulacoseira distans has a much lower density of mantle rows of areolae, the valve face is covered by areolae, thin spines are positioned at the end of each costa, a deep ringleiste is present, and numerous (4-12) prominent rimoportulae are visible in LM (in valve view). In the past, A. pusilla has been misidentified as A. distans, which is probably an extinct species.