While most temperate plants probably underwent glacial constriction to refugia and interglacial expansion, another type of interglacial refugia might have existed to maintain alpine plants during warm periods. To test this hypothesis, we applied phylogeographic methods to 763 individuals (62 populations) which belong to 7 taxonomically difficult species of the Rosa sericea complex distributed in alpine regions of the temperate and subtropical zones in eastern Asia. We used three chloroplast (cp) DNA fragments (trnL-trnF, ndhF-rpl32 and ndhJ-trnF) approximately 3,100 bp and nuclear microsatellite (nSSR) on eight sites to determine whether cold tolerant plants experienced expansion during the Pleistocene. The neutral test and mismatch distribution analysis (MDA) indicated that whole populations and major lineages of the Qinghai-Tibet Plateau (QTP) underwent expansion during the middle to late Pleistocene. Environmental niche modeling (ENM) indicates more suitable habitats during the Last Glacial Maximum (LGM) than at present. We concluded that the demographic history of R. sericea, which diverged in the middle Pleistocene, was mostly affected by climatic oscillations instead of by geographical barriers. The low genetic divergence, as well as the weak phylogenetic structure in the R. sericea complex both support treating this complex as a single taxon.