We analyzed the genetic diversity of eight natural populations of Rosa longicuspis Bertoloni in Yunnan by simple sequence repeats (SSR) markers. The result showed that: 77 alleles were detected by 14 polymorphic SSR primers. At the species level, the Nei's genetic diversity (He) was 0.3139 and the Shannon information index (I) was 0.4747 abundant. It was 65.47% of genetic variation within populations, and 34.53% of genetic variation among populations. So the genetic variation within populations was the main cause of the genetic variation. The Nei’s pairwise genetic identity were 0.7879-0.8986, and genetic distance 0.1070-0.2384. The eight populations were clustered into 3 groups based on genetic distance, showing that the genetic distance was not significantly affected by the geographic distance. The elevation of population growth was positively correlated with He, with the correlation coefficient 0.8771(P＜0.01). The results reveal that the genetic diversity of the populations of Rosa longicuspis Bertoloni in Yunnan is abundant and the genetic variation among populations has medium genetic differentiation. Conservation strategy should be included in situ conservation and ex situ conservation based on the observed genetic information of populations.