Melanochromis mossambiquensis is distinguished from its congeners, except M. auratus, M. dialeptos, and M. wochepa, by a steeper-angled vomer (72–80° vs. 35–53°). It is distinguished from M.

auratus by a mid-lateral and a dorso-lateral black stripe that is narrower than the submarginal black band in the dorsal fin, while in M. auratus the submarginal dorsal stripe is narrower than those on the flank. The

abdominal yellow stripes in M. mossambiquensis are thin and never cover the entire lower abdomen as they do in M. auratus. The lower lobe of the caudal fin contains black spots while that of female M. auratus is yellow without black markings. Male M. mossambiquensis are distinguished from those of M. auratus by the lack of a narrow, yellow mid-lateral stripe. Male M. mossambiquensis are distinguished from those of M. wochepa by a brown/black body with white dorso-lateral and mid-lateral stripes while that of male M. wochepa is blue without stripes. M. mossambiquensis is distinguished from M. wochepa by a shallower body as expressed in a shorter distance between the origins of the dorsal and anal fin (47.1–50.8 % vs. 49.6–54.5 % SL) and a shorter distance between the origins of the dorsal and pelvic fins (27.6–33.4 % vs. 30.1–36.4 % SL), and by a longer lower jaw (29.0–41.5 % vs. 26.7–32.5 % HL). It is distinguished from M. dialeptos by a more elongate body as expressed in a larger distance between the posterior dorsal and the pelvic fin origin

(52.9–60.7 % vs. 49.8–55.8 % SL), a longer snout (29.2–40.3 % vs. 25.9–35.2 % HL), and by fewer rows of scales on the cheek (3 or 4 vs. 4–7).

The populations observed at Metangula and N’kolongwe appear to consist of individuals with longer snouts and shallower bodies (Ref. 80784).