Stauroneis kootenai may be distinguished from Stauroneis gracilior by the lack of hyaline areas adjacent to the stauros. It differs from Stauroneis pikuni by having more robust valves and a smaller size. Stauroneis bryocola has rostrate apices. Stauroneis neohyalina has linear-lanceolate valves, rostrate to subcapitate apices and much finer striae and areolae. Stauroneis subgracilior has smaller valves with very narrow rostrate-capitate apices and very fine striae and areolae. Stauroneis schroederi has very narrow rostrate to subcapitate apices.
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