Abstract: The Hengduan Mountains Region (HMR) is the largest “evolutionary frontier” of the northern temperate zone, and the origin and maintenance of species in this area is a research hotspot. Exploring species-specific responses to historical and contemporary environmental changes will improve our understanding of the role of this region in maintaining biodiversity. In this study, mitochondrial and microsatellite diversities were used to assess the contributions of paleogeological events, Pleistocene climatic oscillations, and contemporary landscape characteristics to the rapid intraspecific diversification of Liangshantriton taliangensis, a vulnerable amphibian species endemic to several sky-island mountains in the southeastern HMR. Divergence date estimations suggested that the East Asian monsoon, local uplifting events (Xigeda Formation strata), and Early-Middle Pleistocene transition (EMPT) promoted rapid divergence of L. taliangensis during the Pleistocene, yielding eight mitochondrial lineages and six nuclear genetic lineages. Moreover, population genetic structures were mainly fixed through isolation by resistance. Multiple in situ refugia were identified by ecological niche models and high genetic diversity, which played crucial roles in the persistence and divergence of L. taliangensis during glacial-interglacial cycles. Dramatic climatic fluctuations further promoted recurrent isolation and admixing of populations in scattered glacial refugia. The apparent mitonuclear discordance was likely the result of introgression by secondary contact and/or female-biased dispersal. Postglacial expansion generated two major secondary contact zones (Ganluo (GL) and Chuhongjue (CHJ)). Identification of conservation management units and dispersal corridors offers important recommendations for the conservation of this species.