Jacks, members of the genus Caranx (Perciformes: Carangidae), comprise economically-important marine fisheries across the world. In the Philippines, this valued fishery extends from the marine environment into a freshwater volcanic lake, Taal Lake. Two jacks, Caranx ignobilis (Forsskål, 1775) and C. sexfasciatus (Quoy and Gaimard, 1825), have long been reported from the lake, with recent molecular evidence alluding to genetic divergence between marine and freshwater populations. Here, a combination of phenotypic features and the mitochondrial Cytochrome oxidase b gene region were used explicitly to profile the taxonomic relationship between marine and freshwater specimens of C. ignobilis and C. sexfasciatus. Using molecular data from all known Philippine Caranx species, a partial phylogeny of the genus was reconstructed and contrasted to observed colouration, morphological and meristic features. Findings include the first report of C. papuensis, in Taal Lake; however, previous reports of C. sexfasciatus are not validated. Caranx ignobilis was confirmed present, yet several morphological features were unique to lake specimens, including red instead of yellow colouration of the lower jaw, anal fins, and caudal peduncle, and four instead of two canine teeth. Further, C. ignobilis sequence distance was 6.3% between marine and lake specimens, whereas C. papuensis distance was 0.2%. The combined molecular and phenotypic data suggest that Taal Lake C. ignobilis may represent an evolutionarily unique lineage. These data are significant for developing management strategies that have typically overlooked the ecological and evolutionary attributes of the jack fishery.