[Objective] This study aimed to analyze the genetic characteristics of Salvia miltiorrhiza by using cpSSR （chloroplast microsatellites） molecular marker method. [Method] Twelve pairs of SSR primers with ideal cpSSR amplification result, good repeatability and clear amplification bands were selected for cpSSR detection and analysis of S. miltiorrhiza samples from 31 sampling locations in 25 counties of 8 provinces in China. [Result] S. miltiorrhiza shows an overall medium level in the cytoplasmic inheritance （cpSSR） and varying degrees of differences in the regions. Based on Shannon’s Information index （I） and Nei’s genetic diversity index, the cytoplasmic genetic diversity in different provinces shows a decreasing order of Shanxi, Henan, Shandong, Hebei, Sichuan, Jiangsu, Shaanxi, Anhui. Genetic variations of S. miltiorrhiza in eight provinces were found mainly among populations. Gene flow among populations with in a province is less than that among different provinces. [Conclusion] Comprehensive analysis shows that S. miltiorrhiza cultivated in genuine producing areas and traditional main producing areas are mainly introduced from the local before introduction of some foreign germplasm resources during cultivation. The exchange of S. miltiorrhiza germplasm resources exists very early among genuine producing areas such as Sichuan, Shandong and Henan, while S. miltiorrhiza germplasm resources in new producing areas are mainly introduced from genuine producing areas. However, no geographical correlation was observed in the genetic differentiation, which further reveals that there is a wide range of genetic exchange among S. miltiorrhiza germplasm resources in China, resulting from the artificial introduction from allopatry.
