Polydactylus longipes n. sp. is described on the basis of three specimens collected from Mindanao Island, Philippines. The species is uniquely distinguished from other Polydactylus species with six pectoral filaments by the length of the latter, the uppermost two extending beyond the midpoint of the caudal peduncle. The new species is further distinguished from other Polydactylus species by the following combination of characters: 13 unbranched pectoral fin rays, six pectoral filaments, 54 or 55 pored lateral line scales, six and 11 scale rows above and below the lateral line, respectively, 31 or 32 gill rakers, vomerine teeth present and grayish-black body.