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The influence of topography and Pleistocenic climatic fluctuations on the population genetic structure of amphibians in the Tsinling-Dabieshan Mountains of China is poorly investigated.Hyla tsinlingensisis a tree frog endemic to the Tsinling-Dabieshan Mountains, with a restricted and patchy distribution that is currently shrinking. We speculated on the evolutionary history of amphibians in this region by studying the population genetic structure ofH. tsinlingensis.Using a total of 212 samples, 32 haplotypes and four haplogroups were found in the present study. Population genetic structure showed significant differentiation (FST) between most populations ofH. tsinlingensisin the Tsinling-Dabieshan Mountains. An analysis of molecular variance (AMOVA) suggested that most of the observed genetic variation occurs between the two regions (the Tsinling and Dabieshan Mountains). Mantel tests indicated that the genetic divergence was induced through isolation by distance. Using Monmonier's maximum difference algorithm to predict the genetic barrier, two putative barriers in gene flow that separate lineages ofH. tsinlingensiswere identified. Mismatch distribution and neutrality tests found a sudden population expansion in all haplogroups except the Tsinling population and total population. This population expansion was identified between 0.5 Myr to 0.1 Myr (Quaternary) by Bayesian skyline plot (BSP). Divergence dating indicated the divergence time between the Tsinling population and Dabieshan population to be 3.26 MYA (Pliocene). In conclusion, the topography of the Tsinling and Dabieshan Mountains exerts a significant impact on the population genetic structure ofH. tsinlingensis,and climatic oscillations during glacial periods in the Quaternary affected the distribution ofH. tsinlingensis. [ABSTRACT FROM AUTHOR]