We use discrete morphological characters in a statistical framework to reassess the taxonomic status of the Palawan pangolin Manis culionensis relative to the Sunda pangolin M. javanica. We recommend that the 15 species-level traits previously proposed in the literature to distinguish the 2 pangolins be replaced by 5 newly defined diagnostic characters related to skull and external scales. Our study supports species-level partition between the Palawan and Sunda pangolins at a frequency of expected polymorphism threshold fixed to 0.10. Isolation through sea level rising (approximately 800,000–500,000 years ago) of proto-Palawan pangolins coming from Borneo through Early Pleistocene land bridges might have promoted the speciation of M. culionensis, a Palawan endemic species to be considered of high conservation concern.