Hypopygus nijsseni is diagnosed from congeners by the following combination of characters: the total number of anal-fin rays (145–152 versus 102–135 in H. hoedemani, H. lepturus, and H. minissimus; 155–174 in H. cryptogenes), the presence of the sixth infraorbital bone (versus absence in H. hoedemani, H. lepturus, and H. minissimus), the presence of oblique bands (versus absence in H. minissimus), the presence of scales at midbody (versus absence in H. minissimus), the dorsal rami of intermittent branch of anterior lateral line nerve visible as two black parallel lines (versus not visible in H. ortegai), the head length (13.2–15.3% of LEA versus 12.6–13.9 in H. ortegai), the distance at the nape (12.5–13.8% of LEA versus 11.0–12.5 in H. ortegai), the total number of pectoral fin rays (ten to 12 versus 12–16 in H. isbruckeri), the number of scales above the lateral line (five to six versus seven to eight in H. isbruckeri), and the distance from the anus to the anal fin (7.9–9.4% of LEA versus 10.0–12.0 in H. neblinae) (Ref. 88778).