Schistura pantherina differs from S. xhatensis in having shorter black spots/blotches along the side of the body and a much shorter vertical black basicaudal bar that spans only the medial rays; in S. xhatensis, the basicaudal bar spans all but the upper-most and lower-most rays. Schistura xhatensis has a conspicuous black blotch at the dorsalfin origin followed by a smaller red spot, which S. pantherina lacks. Schistura pantherina also differs from S.xhatensis in having a complete (vs. incomplete) lateral line, a shorter prepelvic length (48–51% vs. 54% SL), 11 pectoral rays (vs. 9–10), and 8 pelvic rays (vs. 6 or 7).