Rosa roxburghii Tratt. is a well-known commercial horticultural crop in China with nutritional and medicinal value. Wild germplasms of this species are mainly distributed in Southwest China but the population is decreasing due to continuous exploitation, habitat destruction, and fragmentation. Therefore, assessing the genetic diversity and phylogeography is essential for efficient conservation. Herein, two chloroplast intergenic spacers (trnL-trnF and accD-psaI) were investigated in 255 individuals from 29 R. roxburghii populations and 18 haplotypes (H1–H18) were identified. High levels of haplotype diversity (H_d = 0.829) and nucleotide diversity (π = 1.3 × 10⁻³) were detected in these populations. Also, the genetic variation representing 86.4% of the total variation was detected by an analysis of molecular variance. A significant correlation was established between genetic divergence and geographic distance by the Mantel test (r = 0.204, P = 0.04, 9 999 permutations), suggesting the isolation-by-distance model. A significantly higher N_st than G_st (N_st = 0.257, G_st = 0.136, P < 0.05) indicated the phylogeographic structure of R. roxburghii. Further phylogeographic analysis revealed rapid range expansion in the population, probably between 647 073 and 217 848 years ago. The primary processes shaping the genetic patterns of the R. roxburghii populations included restricted gene flow with isolation distance within clades 1-8, 2-3, and overall, contiguous expansion within clades 1-3 and 3-2, past fragmentation, and/or long-distance colonization within clades 1-9 and 2-2. Conservation priority should be given to the core populations GZ, FQ, DF, DS, xy, AL, LC, PB, and XY in the Yunnan-Guizhou Plateau, NZ and MX in the Qingling-Bashan mountains, and MN in the Hengduan mountains, where an in situ preservation and management strategy should be applied.