Rasboroides nigromarginatus is distinguished from its congener R. vaterifloris by having the dorsal profile of the head slightly concave (vs. approximately straight) behind the level of the eye in males; base of the pelvic fin closer to origin of anal fin than to base of pectoral fin (vs. located midway between pectoral-fin base and anal-fin origin); and dorsal margin of operculum with a deep indentation (vs. dorsal margin of operculum approximately straight). Male R. nigromarginatus differs from male R. vaterifloris by possessing a lesser interorbital width (17-22 % HL, vs. 29-33) and a lesser internarial width (11-17 % HL, vs. 19-21), while females differ by having a lesser anal-fin depth (17.4-22.7 % SL, vs. 23.5-24.8), a lesser interorbital width (16-21 % HL, vs. 25-33), a lesser caudal-peduncle depth (10.4-12.3 % SL, vs. 12.4-13.4) and a greater caudal-peduncle length (21.1-25.0 % SL, vs. 18.6-21.2). It can be differentiated from R. pallidus and R. rohani by having the dorsal-fin origin 1 scalewidth (vs. 3 scale widths) behind pelvic-fin origin; and a body depth of 26.9-33.0 % SL (vs. 33.0-37.5 in R. pallidus and 33.3-40.0 in R. rohani) (Ref. 94541).