Hypopygus isbruckeri is diagnosed from congeners by the following combination of characters: the total number of anal-fin rays (136–156 versus 102–135 in H. hoedemani, H. lepturus, and H. minissimus), 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 total number of pectoral fin rays (12–16 versus 10–12 in H. nijsseni), the number of scales above the lateral line (seven to eight versus five to six in H. nijsseni, and three to five in H. neblinae), the head length (13.2–22.9% of LEA versus 12.6–13.9 in H. ortegai), and the dorsal rami of intermittent branch of anterior lateral line nerve visible as two black parallel lines (versus not visible in H. ortegai) (Ref. 88778).