Abstract Clematis sibirica, a woody vine occurring primarily under conifer forests, is widespread in northern Eurasia. In this study, we intend to illustrate how the taxon has responded in the area of the Tianshan and Altai Mountains of Central Asia to the Pleistocene climatic fluctuations. The chloroplast intergenic spacer psbA-trnH was sequenced for 125 individuals from 28 populations, and a total of eight chlorotypes were identified. The presence of definite phylogeographic structure was detected for the species (NST > GST, P < 0.001), and phylogenetic analysis indicated that the eight chlorotypes were clustered into two divergent lineages. They split at approximately 550–690 ka BP, according to coalescence analysis, coincident with the Pleistocene maximum glacial stage in these mountains, which suggests the restriction of these lineages to separate refugia at that time. Spatial analysis of molecular variance likewise divided the sampled populations into two associations, an Altai and eastern Tianshan group (populations 1–17), and a western Tianshan group (populations 18–28). Low levels of genetic diversity and unimodal mismatch distributions were obtained for both of these groups, suggesting postglacial range expansions. During the course of these expansions, mountain ranges surrounding the Dzungarian Basin probably served as migration corridors. In addition, a contact zone was identified in the central Tianshan and eastern Altai Mountains between the two phylogeographic lineages.