Aim: The aim of this study was to conduct comprehensive phylogeographic and demographic analyses to examine the degree to which topographic and climatic conditions have affected the patterns of diversification and migration in a strictly montane inhabitant, the montane long-tailed mole (Scaptonyx fusicaudus). Location: The mountains of south-western China and adjacent mountains including Mts. Bashan, Dalou and Qinling also known as the sky islands in south-western China. Taxon: The long-tailed mole (S. fusicaudus), a semi-fossorial mammal distributed in the sky islands of south-western China, is a relict species and the sole representative of the tribe Scaptonychini. Methods: We sequenced one mitochondrial and six nuclear genes from 113 samples across the species’ range. We estimated phylogenetic relationships and divergence times, conducted genetic structuring and species delimitation using multiple approaches and used Approximate Bayesian Computation to test potential gene flow. We conducted ecological niche modelling to predict the species’ potential distribution in the present, the last glacial maximum and the last interglacial (LIG). Results: The species comprises a minimum of 17 operational taxonomic units which are isolated in different mountain ranges. The lowlands and large rivers act as barriers to dispersal, and have isolated evolutionary lineages for up to 11 million years. Long-distance dispersal is evident among a few discrete montane archipelagos. Suitable climatic conditions during the LIG are limited to only a few sites, thus geographically restricting climatic stable areas across geological periods (from the LIG to the present). Main conclusions: For low-vagility species, the complex topography of the sky islands has promoted exceptional diversification through a combination of eco-environmental stability as well as geographic fragmentation. The mountains have acted as a buffer against climate change, and have provided continuously suitable habitats for S. fusicaudus since the early Late Miocene, supporting the hypothesis that the sky islands constitute “museums” of ancient lineages. Lowlands and river valleys have acted as barriers preventing gene flow, while the montane archipelagos could have provided stepping stones to facilitate dispersal.