To explore the evolutionary consequences of climate-induced fluctuations in presently fragmented temperate forest habitats in continental East Asia we investigated the phylogeography and demographic history of the temperate-deciduous forest endemic Dysosma versipellis from disjunct montane sites in Central-Southeast China. Based on a survey of chloroplast (cp) DNA sequence variation, our analyses show that this perennial herb consists of morphologically indistinguishable western and central/eastern cpDNA lineages. Coalescent analyses under the 'isolation with migration' (IM) model support an ancient (Mid-Pleistocene) divergence between these lineages, with the western lineage having persisted without significant population growth in a long-term refuge just east of the Tibetan (Qinghai-Xizang) Plateau. In contrast, for the central/eastern lineage, we found strong evidence for population expansion from a refuge located south of the middle and lower reaches of the Yangtze River, and likely coinciding with the last or penultimate interglacial, followed by considerable population isolation and divergence in situ over (at least) the latest glacial-interglacial cycle. In line with recent evidence from palaeomodeling of East Asian forest biomes, our results suggest that the same vicariance factor, i.e. climate-induced eco-geographic isolation through (a)biotic displacement of temperate-deciduous forested habitats, promoted the divergence of D. versipellis lineages and populations at different spatial-temporal scales and over glacial and interglacial periods. Thus, there is no evidence that populations of D. versipellis merged at lower elevations during the last glacial(s). As such, D. versipellis accords with the premise that Late Quaternary refugial isolation is likely to have enhanced allopatric (incipient) species formation of temperate plants in East Asia.