Abstract: Bretschneidera sinensis Hemsl. is a rare plant species mainly distributed in China. In this study, amplified fragment length polymorphism (AFLP) data were used to analyze genetic diversity, genetic structure, and phylogeography of this species. A total of 192 individuals from 24 populations in 11 provinces were sampled. Results showed a relatively high level of genetic diversity for B. sinensis, with an expected heterozygosity (He) and Shannon's diversity index (Ⅰ) of 0.2728 and 0.4070, respectively. Relatively high genetic differentiation (G_ST=0.7138) and lower gene flow (N_m=0.2005) among B. sinensis populations were detected. The infra-population genetic variations were significantly greater than the inter-population variations. Four phylogeographic groups were discovered from cluster, STRUCTURE, and BAPS analyses. Populations in the East Yungui Plateau showed high levels of genetic diversity with unique hereditary constitution. This area is a possible diversity center and glacial refuge for B. sinensis in China, which expanded northward, eastward, and southeastward after the last ice age. Populations from the Nanling Mountains, with a close relationship to their neighbor population, had higher genetic diversity than other areas. The Nanling Mountains are another probable glacial refuge in the evolutionary history of B. sinensis.