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Aim The Himalaya-Hengduan Mountain (HHM) biodiversity hotspot including the 'sky islands' of Southwest China harbour exceptional plant diversity and endemicity at subnival summits (most of them exceeding 4300 m a.s.l.). This study is the first using a comparative phylogeographical framework to gain insights into the temporal origin of this highly fragmented subnival flora, and the historical factors shaping its genetic architecture as exemplified by four perennial herbs. Location Himalaya-Hengduan Mountains, China. Methods Based on nuclear and/or chloroplast (cp) DNA sequences for each of the four studied species, we performed AMOVA and mismatch distributional analyses to assess molecular structure, diversity and demographic history in relation to current and last glacial distributions using ecological niche modelling (ENM). Time-calibrated phylogenetic reconstructions of cpDNA data were used to infer species-specific stem and crown ages. Results Our time estimates suggest that these species originated during the Late Pliocene or early-to-mid Pleistocene, whereas their onset of diversification generally falls into the mid-Pleistocene. All four species exhibited island-like population genetic structures, with all of them showing signatures of recent population growth and/or spatial expansion based on cpDNA. By contrast, ENM indicated that species broad-scale distributions remained fairly stable over the last glacial/post-glacial cycle. Main conclusions The temporal origin of the four subnival HHM species is likely associated with tectonic changes in the region, while their near-simultaneous onset of diversification during the 'Naynayxungla Glaciation' (0.72-0.50 Ma) could reflect initial population divergence through climate-induced habitat fragmentation. Despite a rather stable distributional history, geographical population isolation and localized range expansion/contractions likely resulted in significant genetic structure and differentiation over the last glacial/ post-glacial cycle. Overall, the present results are strongly indicative of shared evolutionary histories and phylogeographical structures among subnival plants from the 'sky island system' of the HHM region. [ABSTRACT FROM AUTHOR]