Stauroneis intricans has a smaller maximum size, straight proximal raphe ends, and higher areola density. Stauroneis jarensis has straight proximal raphe ends and expanded proximal pores. Stauroneis anceps has more narrow apices. Stauroneis fluminea and S. pergracilis have straight proximal raphe ends and generally larger valves, although size ranges of the three species do overlap. Stauroneis vandevijveri has more lanceolate valves and straight proximal raphe ends.