The new species belongs to the anchovy family and shares several traits with two other species, including a long maxilla, an indented rear edge of the preopercle and specific counts of anal-fin rays and lower gill rakers.

Stolephorus lotus differs in having 37–39 scale rows along the body and 20 or 21 predorsal scales. Its anal fin also begins farther forward, below the sixth to eighth dorsal-fin rays rather than below the eighth to tenth rays seen in the other two species.