AbstractIntegrative taxonomy reveals a new troglophilic species of Schistura, from a cave‐dwelling population inhabiting stream draining (Barak–Surma–Meghna drainage) through the Krem (=cave) Mawjymbuin in East Khasi Hills of Meghalaya. Morphologically, the new species is easily distinguished from its congeners in having a combination of characters, including a unique colour pattern in the form of 14–20 greyish black to faint black bars overimposed to a black midlateral stripe on a greyish brown to pale beige (yellowish green in life); pre‐dorsal bars thin, numerous, wider than interspaces, weakly contrasted, sometimes broken and/or incomplete; bars posterior of anal‐fin base numerous and variable, mostly broken or incomplete, located on lower flank, weakly contrasted; a complete lateral line; presence of an axillary pelvic lobe; an uninterrupted thick black stripe along the base of the dorsal fin; an incomplete black basicaudal bar, dissociated, occupying median one‐third of caudal‐fin base; conspicuous black botch on the procurrent rays of the upper lobe of the caudal fin; and a type of sexual dimorphism: males with slender body, bars mostly irregular on flanks and slightly puffy cheek with greater lateral head length; females with regular‐shaped bars and swollen body. Analysis of the mitochondrial cytochrome c oxidase I (COI) gene sequence of the new species shows significant genetic divergence with p distances ranging 4.5%–13.6% from its sister species found in northeast India, supporting its report as new species. Further, this finding is also validated by phylogenetic analysis and the species delimitation approaches, Assemble Species by Automatic Partitioning (ASAP) and Poisson Tree Processes (PTP), which clearly resolved that the Schistura densiclava sp. nov. is distinct from its sister species. Although the species has been sampled from the cave, it retains a fully pigmented body and functional eyes, which are not reduced when compared to other epigean Schistura, tentatively indicating it as a troglophile. Distribution of the new species is limited to the cave, which suggests an endemism in this cave system.