Abstract Background and Aims Many plant taxa in the Qinghai–Tibetan Plateau (QTP) and the Hengduan Mountains (HM) radiated rapidly during the Quaternary but with frequent secondary contact between diverging populations. Incomplete lineage sorting and introgressive hybridization might be involved during the rapid radiation, but their effects on phylogeography have not been fully determined. Methods We investigated the chloroplast DNA (cpDNA)/internal transcribed spacer (ITS) sequence variations of 611 samples of Rhodiola bupleuroides, R. discolor, R. fastigiata and R. chrysanthemifolia from the QTP and HM to compare the phylogeographic patterns between the four species with different evolutionary histories, geographic ranges and reproductive modes. Key Results The divergence times of these species were consistent with the last peak of in situ speciation in the HM. While closely related species exhibited different phylogeographic patterns, they shared several ribotypes and haplotypes in sympatric populations, suggesting introgressive hybridization. A significant phylogenetic discordance between ribotypes and haplotypes was detected in three species, implying incomplete lineage sorting. Rhodiola discolor houses an extraordinary richness of cpDNA haplotypes, and this finding may be attributed to adaptive radiation. Conclusion In addition to geographic isolation and climate oscillations during the Quaternary, both introgressive hybridization and incomplete lineage sorting play important roles in species that experienced rapid diversification in the QTP and HM.