Hemigrammus diagonicus can be easily differentiated from its congeners, except for Hemigrammus silimoni, by the presence of a blotch on the caudal fin restricted to the dorsal lobe (vs. no blotches on the caudal fin, blotches restricted to the base of the rays, or blotches arranged symmetrically in dorsal and ventral lobes). Hemigrammus diagonicus is distinguished from H. silimoni by the autapomorphic presence of the caudal-fin blotch shaped like a bar that extends diagonally from the base of the median rays to the end of the upper lobe rays (vs. conspicuous ocellus like blotch on the lower region of the caudal-fin dorsal lobe); height of dorsal fin 22.3–30.2% SL (vs. 31.0–37.4% SL); length of anal-fin base 24.0–28.0% SL (vs. 28.7–31.5% SL); horizontal eye diameter 33.8–41.3% HL (vs. 43.4– 48.1% HL) (Ref. 87304).