Brachysira brebissonii is distinguished from small forms of B. hannae by a lower stria density and less radiate striae near the central area. Brachysira brebissonii has larger areolae, a lower stria density and a smaller central area compared to smaller valves of B. styriaca. Brachysira brebissonii has a more distinct lanceolate valve and larger areolae compared to smaller valves of B. zellensis. Brachysira brebissonii is most similar to B. lehmanniae, a species described from South America. Brachysira brebissonii is distinguished by large areolae that extend along the axial area and less radiate striae near the central area.