We report the first records of Nyctalus plancyi from the Philippines, on the basis of three specimens taken in high-elevation mossy forest in the Central Cordillera of northern Luzon. We also report three new specimens of Falsistrellus petersi in the same areas, previously a poorly known species within the Philippines, and provide the first genetic data on the phylogenetic position of the genus. Analysis of sequence data from the mitochondrial gene cytochrome b shows ca. 4% divergence of the Philippine N. plancyi from a sample from China. Combined sequence data from cytochrome b and the nuclear gene RAG2 confirm that JV. plancyi is related to Pipistrellus. They further show that F. petersi is related to Hypsugo and Vespertilio, and Philetor brachypterus is related to Tylonycteris, with all of these taxa being members of the Vespertilionini, not the Pipistrellini. Nyctalus plancyi is the first mammal species documented to have colonized the main, oceanic body of the Philippines from the north (i.e., Taiwan or mainland China), rather than from the south (Borneo, Sulawesi, or New Guinea).