Melanochromis wochepa is distinguished from its congeners, except M. auratus, M. dialeptos, and M. mossambiquensis, by a steeper-angled vomer (72–80° vs. 35–53°). It is distinguished from M. auratus, M. dialeptos, and M. mossambiquensis by the male coloration pattern which is blue without white stripes and which is brown/black with yellow and pale-blue stripes in males of the other species. Female M. wochepa are distinguished from M. auratus by a submarginal dorsal band that is wider than the mid-lateral and the dorsolateral stripe. The abdominal yellow stripes in female M. wochepa are thin and never cover the entire lower abdomen, while those in female M. auratus usually cover the entire lower half of the body. M. wochepa is further distinguished from M. dialeptos by a longer head (30.2–33.3 vs. 29.8–31.4 % SL), a deeper body (30.2–34.7 vs. 26.8–31.8 % SL), by a larger distance between the posterior dorsal and pelvic fin (53.3–59.8 % vs. 49.8–55.8 % SL), by a longer pectoral fin (22.8–33.0 % vs. 19.5–24.3 % SL), and by more dorsal-fin rays(7–10 (mode 9) vs. 7–9 (mode 7)). It is further distinguished from M. mossambiquensis by a deeper body as expressed in a larger distance between the origins of the dorsal and anal fins (49.6–54.5 % vs. 47.1–50.8 % SL) and a larger distance between the origins of the dorsal and pelvic fins (30.1–36.4 % vs. 27.6–33.4 % SL), and by a shorter lower jaw (26.7–32.5 % vs. 29.0–41.5 % HL).