A combined approach using molecular and morphological data has revealed that the taxon Myotis taiwanensis, which until now has been usually considered as a subspecies of Myotis adversus, should be reinstated as a full species, as originally described by Ärnbäck-Christie-Linde (1908) from Takao, Anping, Tainan, Formosa (= southern Taiwan). In our genetic analysis using two nuclear DNA segments of protein kinase C iota (PRKCI) and ubiquitin specific peptidase 9 (Usp9x), X-linked genes, together with two mitochondrial genes, i.e., nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) and cytochrome b (Cyt b), we demonstrate that M. taiwanensis is closely related to M. pilosus, and largely divergent from two subspecies of M. adversus. Our analysis further shows that M. taiwanensis differs considerably from M. adversus in external and dental features. New records of M. taiwanensis from Shandong and Anhui provinces in eastern China are presented.