Recent molecular phylogenetic studies of Southeast Asian shrews (Crocidura) suggest that Crocidura mindorus, as currently defined, is diphyletic. The species is reported from Mindoro (type locality) and Sibuyan islands in the Philippines, each of which has been isolated from other land masses over considerable geological timescales. We examined morphological evidence to determine whether the Mindoro and Sibuyan populations represent distinct, endemic species. We found that the two populations differ in discrete and mensural characters. This evidence, combined with previous molecular phylogenetic studies, confirms that the Sibuyan population is an isolated, independently evolving lineage, and we formally describe it as a new species, Crocidura ninoyi.