Climate oscillations and landscape heterogeneity make the historical population processes of organisms of the Qinghai-Tibet Plateau quite complex. We used chloroplast DNA sequences and amplified fragment length polymorphism (AFLPs) to study the phylogeography and genetic variation of the Qinghai-Tibet Plateau endemic Spenceria ramalana Trimen. The parsimony network contains two star-like evolutionary units, nested into two nested clades, coinciding with geographic population groups indicated by SAMOVA software. The central group shows genetic homogeneity, indicating a bottleneck or founder effect of population dynamics. Margin groups contribute more haplotype diversity (C-T), indicating potential refugia. Several expansion events during several interglacial periods were detected. The latest expansion of the eastern population contributed to the modern population structure of the central area. Four AFLP clusters were detected. Higher C-T, a relict pattern of haplotype distribution and DW values of marginal populations, confirmed the location of potential montane refugia. Relict distribution pattern, nested clade phylogeographic analysis conclusions, and restricted gene flow detected by AFLPs indicated an isolation pattern of the populations of montane areas. Heterogeneity of landscape of the western and southern montane areas could be the main barrier for gene flow. Moisture conditions and ecotype transformation might help to build the phylogeographic pattern of this species. Neither chloroplast DNA markers nor AFLP was able to differentiate the two varieties of this species.