Taxonomic analysis of four specimens of Macrognathus collected from Manimala River in Kerala reveals that they present several meristic and morphological differences from their relative species. The new species is diagnosed by a combination of the following characters: 2830 dorsal spines; 2627 distinct, yellow, vertical lines present on lateral sides, originating from mid dorsal line to ventral side; between every two yellow lines 89 small whitish yellow round spots in a row; spinous part of dorsal fin originating at the level or slightly behind the end of pectoral fin; a small round black spot present at the base of pectoral and caudal fin; the latter with 1013 rays. Macrognathus fasciatus, the new species, is described and compared with its congeners.