Arceuthobium sichuanense belongs to semiparasitic seed plants. To explore the genetic diversity of A. sichuanense and its relationship with the host selection and geographic distribution, we collected 100 samples on 5 species of Picea from 3 sites which distributed in Sichuan, Gansu and Qinghai provinces, and molecular marker of A. sichuanense was conducted by ISSR technology. The results demonstrated that 130 bands were amplified by 10 primers, among which 129 bands were polymorphic, accounting for 99.23%. Genetic diversity analysis showed Neis genetic diversity (H_e) was 0.313 9 and Shannons genetic information index (I) was 0.476 5, indicating that the genetic diversity among 100 samples was abundant. Gene flow among A. sichuanense populations was relatively weak (N_m=0.528 7), which might limited the genetic differentiation among the populations (G_st= 0.486). The unweighted pairgroup method with arithmetic average (UPGMA) dendrogram classified the 100 strains into two major groups. The two groups could be further divided into 3 and 2 subgroups, respectively. Based on the different hosts, A. sichuanense grown on P. asperata and P. likiangensis var. balfouriana clustered into the first group, and the others clustered into the second group. The result indicated that geographical isolation and host selection played an important part in the genetic diversity of A. sichuanense.