A new species, Johnius medidentatussp. nov., is described based on specimens collected from trawl and gill net landings along both the east and west coasts of India. The new species belongs to the subgenus Johnieops and can be distinguished from its close congeners, Johnius borneensis and Johnius dussumieri, by a combination of morphological characters, including an oval-shaped body (vs. oblong in the other two) and moderately sized, enlarged teeth in the inner row of lower jaw (vs. much enlarged and well differentiated in J. borneensis, and enlarged but weakly differentiated in J. dussumieri). It differs further from J. borneensis by the absence of much enlarged anterior teeth in the outer row of upper jaw (vs. present), snout rounded from dorsal view (vs. pointed), relatively shorter snout length (15.3–22.9% HL vs. 20.4–26.2% HL), higher modal number of total gill rakers (21 vs. 17). From J. dussumieri, it can be distinguished by a longer pre-anal length (68.5–73.5% SL vs. 59.8–69.9% SL) and larger eye diameter (21.8–30.1% HL vs. 15.7–22.4% HL) . The new species can be easily distinguished from J. plagiostoma found in Indian waters in having first pair of mental pores in a false pit on the underside of the head (vs. separated by symphysis), absence of mental process on the lower jaw (vs. present), higher modal number of scales below the lateral line (12 vs. 10) and fewer modal number of total gill rakers (21 vs. 25). Mitochondrial COI gene analysis revealed over 8% divergence from its congeneric species. Maximum Likelihood phylogenetic analysis supports the distinctiveness of J. medidentatussp. nov., placing it in a well-supported clade closely related to J. borneensis.