Abstract: Genetic diversity and genetic structure of 5 Reaumuria soongorica populations from Gansu (total about 50 individuals), were analyzed by ISSR (inter simple sequence repeat) markers. Twelve highly stable and repeatable ISSR primers (selected from 50 primers tested) detected a total of 69 loci of which 60 were polymorphic (86.96% of the total). The PCR products ranged from 500 to 3 000 bp. At the species level, the Shannon index (I) was 0.542 9, Nei’s gene diversity index (H) was 0.379 0, the coefficient of gene differentiation (G_st) was 0.096 4, and the gene flow (N_m) was 4.685 1. The software Popgen 32 analysis of the results showed that there was more genetic differentiation within populations than between populations. At the population level, I and H were 0.489 3 and 0.342 4, respectively. All of these results showed that R. soongorica has a high genetic diversity in Gansu. Cluster analysis showed no direct correlation between genetic distance and geographic distance, suggesting that genetic diversity of R. soongorica in Gansu was possibly related to species traits and communities.