Aulacoseira ambigua differs from other species of the genus by the hollow ringleiste. In cell dimensions and proportions it is similar to A. subarctica and A. granulata.
Aulacoseira granulata and A. granulata var. angustissima can be easily distinguished by their long separation spines and large square mantle areolae.
Aulacoseira subarctica has large spines originating from two pervalvar costae on both separation and linking valves, while A. ambigua has small bifurcate linking spines originating from each pervalvar costa. It may be difficult to distinguish separation valves of A. subarctica and A. ambigua because the pervalvar costae in valves of A. ambigua often coalesce at a distance to the valve face. As a result, the separation spines appear to originate from two costae as in A. subarctica. Separation spines of A. ambigua are, however, much thinner than those of A. subarctica.