To understand the environmental effects on adaptations of Caragana davazamcii Sancz, we selected five habitats along a precipitation gradient from east to west of the Erdos plateau to quantitatively examine the genetic characteristics of of Caragana davazamcii population using the ISSR markers. Fresh leaves of individual plants were collected and dried with silica gels. 20 individuals were sampled randomly from per habitat. We found that the Nei’s gene index and Shannon’s diversity index increased with decreasing in precipitation. The total genetic diversity of five populations (H_T) was 0.2963; genetic diversity within populations（H_s）was 0.2269; genetic diversity among populations (D_ST) was 0.0594; genetic differentiation coefficient (G_ST) was 0.2005; and gene flow was 1.9936. We also found that 79.95% of molecular variation in C davazamcii existed within populations, while small among populations-suggesting a strong and active hybridization. The genetic distance between five populations was small but increased gradually with changes of the habitats from east to west (i.e., high to low precipitation) while genetic identity decreased. All these indicated that precipitation that has a long-term effect on moisture may also affect genetic diversity of C davazamcii.