Stauroneis pikuni lacks the hyaline areas in the striae adjacent to the central area that are characteristic of Stauroneis gracilior. It is also larger than S. gracilior and has somewhat finer (more closely spaced) striae and puncta. Stauroneis pikuni has larger and more gracile valves than S. kootenai. Stauroneis neohyalina has linear-lanceolate valves and much finer striae and puncta. Stauroneis schroederi has strictly lanceolate valves with very narrow rostrate to subcapitate apices.