To investigate the mechanisms responsible for the high diversity in central and adjacent southwestern China, we inferred the phylogeographic history of Primula ovalifolia from chloroplast DNA data. One hundred and thirty five individuals from 13 natural populations (including one Primula tardiflora population) were analyzed. A total of 23 haplotypes were identified. Most of them were exclusive to a single population. Strong phylogeography structure was detected, with NST (0.936) significantly higher than GST (0.784). Phylogenetic analysis showed that all haplotypes were clustered into three lineages (clades I, II, and III). High genetic diversity was revealed, possibly due to the interglacial contraction and glacial expansion. The three identified lineages may have undergone different historical processes after the mid-Pleistocene, due to their early divergent time. Multiple refugia were inferred for the three lineages. Pleistocene climatic oscillations, combined with the complex local topography, were responsible for the strong phylogeographic pattern of P. ovalifolia. Our analysis supports the hypothesis that the central and adjacent southwestern region of China was an important refugium for the survival, persistence, and further speciation of most East Asia flora, which has led to high species diversity in this region.