Cymbella mexicana is differentiated from C. janischii by the size of the valve and features of the raphe. Cymbella janischii valves are larger in length and breadth than those of C. mexicana. In addition, the proximal raphe ends of C. janischii are larger than those of C. mexicana. The terminal fissures of C. janischii are dorsally deflected ~60º, whereas those of C. mexicana are dorsally deflected nearly 90º.