: Objectiv To analyze the genetic polymorphism and relationship of Sinopodophyllum hexandrum from Gansu and Qinghai province in China, and to offer some information for the domestication and protection of wild Sinopodophyllum hexandrum. Methods ISSR primers were used to analyze the genetic diversity of 11 populations of Sinopodophyllum hexandrum. Cluster analysis of the unweighted pair-group method with arithmetic average (UPGMA) and do Mantel test with geographic distance, out based on the molecular data obtained, and a dendrogram was constructed. Results Totally 155 alleles were amplified using the 11 ISSR primers. The number of alleles in per primer range was 10-17, with an average of 14.1 and 1320 polymorphic locis. The average percentage of polymorphic loci (PPL) was 65.50%. The Nei’s gene diversity (H) and Shannon’s information index (I) were 0.2101and 0.3191. The genetic distances range was 0.0316-0.3769,and Mantel test p=0.4220. Conclusion The genetic polymorphism among 13 populations of Sinopodophyllum hexandrum is relatively abundant and the gene flow within the populations were very rich, the genetic differentiation within the population is significantly greater than the differentiation between populations and there is no relationship between genetic distance.