Differs from both Mystus castaneus and Mystus nigriceps in having a second posterior fontanel on the supraoccipital. It further differs from Mystus castaneus in having a shallower adipose fin (4.7-6.0% SL vs. 6.1-7.0), smaller serrations on the posterior edge of the pectoral spine (maximum height of serrations 3.6-4.8% of spine length vs 6.9-8.0) and a more deeply forked caudal fin with a more slender upper lobe. Further differs from Mystus nigriceps in having a longer adipose fin base (31.6-36.1% SL vs 26.3-31.4), longer second and third dorsal fin rays, causing the dorsal fin to appear less rounded, and a brown body with a distinct darl triangular patch on the base of the caudal peduncle (vs. greenish gray body with a diffuse dark triangular patch on the base of the caudal peduncle).