Navicula margalithii is most similar to N. tripunctata. N. margalithii, however, possesses a strongly asymmetrical central nodule, a small central area and the lineolate areolae are longer. Navicula recens has shorter and more lanceolate valves and strongly radiate striae. N. geronimensis has asymmetrical central area and central raphe endings sharply bent to the primary side of the valve.