Mystus nanus can be diagnosed from all congeners from India and Sri Lanka except

M. bleekeri, M. carcio, M. tengara, and M. vittatus by having two distinct cream stripes along the entire length of the flank (vs. stripes absent on body). It is distinguished from the four named striped species by the combination of the following characters: eye diameter (19-22 % HL); maxillary barbel extending up to or slightly beyond origin of anal fin; distal margin of dorsal fin rounded; adipose-fin base length 25.3-31.4 % SL; serrae along posterior margin of pectoral fin 9-12; sclera blackish grey in preserved specimens; and posterior cranial fontanelle ending about one eye-diameter anterior to the base of the supraoccipital process (Ref. 116163).