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Mountains, representing storehouses of biodiversity, endemism and threatened species, are biodiversity hotspots of great conservation importance. However, increasing evidence indicates that mountain species throughout the world are responding to climate change, past or contemporary, by shifting their geographic distributions and patterns of genetic diversity, potentially affecting their adaptive capacity and increasing risk of extinction. Using the iconic high-elevation frog Nanorana parkeri as indicator, we showed how spatial analyses of climatic stability combined with genetic data allow unravelling amphibian responses to past and future climate changes on 'the roof of the world'-the Qinghai-Tibetan Plateau. We found that areas along the Yarlung Tsangpo Valley were climatically more stable relative to other regions, apparently serving as a large climatic refugium during Quaternary glaciations, but that these areas will likely be affected by future climate change. As populations closer to Quaternary refugia usually had higher genetic diversity, current genetic diversity can be explained in the largest part by distance to historically stable areas, outweighing other historical and contemporary factors. Along with the dynamics of suitable range, a fluctuating habitat fragmentation supported the pattern of historical changes in genetic diversity (N-e) over time. Our results emphasize strong relationships between amphibian genetic diversity, past range dynamics and where to preserve suitable habitats in the face of future climate changes. More generally, our findings highlighted a central role of refugia during Quaternary climatic fluctuations, and how isolation from refugia may have modulated amphibian genetic diversity across the Qinghai-Tibetan Plateau.