Abstract: AIM To discuss the genetic differentiation between wild and cultivated populations of Paeonia lactiflora Pall., and to find the reason for forming the genuineness of Radix Paeoniae rubra (Chishao) and Radix Paeoniae alba (Baishao). METHODS Forty three representative samples of P.lactiflora from 11 localities were analyzed by RAPD method with 21 random primers. According to RAPD results, the genetic diversity and genetic differentiation of P.lactiflora were detected by the percentage of polymorphic sites (PPB), the coefficient of gene differentiation (G_ST) and analysis of molecular variance (AMOVA). RESULTS(1) At species level, the PPB of P.lactiflora was 85.26%, the Nei's gene diversity (H_t) was 0.166. The PPB in wild population (WP) was 77.61%, which was more than that (54.96%) in cultivated population for medicine (MP), and that (61.76%) in cultivated population for ornament (OP). (2) AMOVA showed that 29.50% of the genetic diversity resulted from differentiation among populations. Pairwise Phist distance (0.3632) between WP and MP was furthest, while that (0.0973) between MP and OP was closest, indicating population differentiation was significant (P<0.001). (3) In general, cluster analysis revealed that the samples of P.lactiflora were divided in wild and cultivated groups (except for 39). In WP, individuals of Duolun were separated from those of other localities. In MP, the clusters of samples corresponded well with their own habitats. CONCLUSION In addition to environmental factor, genetic differentiation should be the main cause for the genuineness of “Chishao” and “Baishao”. Because of over collection and worse habitat, P.lactiflora in Duolun, whose root is the famous Chinese Geo-herbal “Duolun Chishao”, is progresively rare. So, it should become the endangered germplasm resource to protect.