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[Objective] Study on the genetic diversity in wild populations of Poacynum hendersonii. [Method] Random amplified polymorphic DNA (RAPD) technique was employed to analyze the genetic diversity in five wild populations of P. hendersonii sampled from Xinjiang, Gansu and Qinghai provinces. [Result] Totally 165 clear and repeatable bands were generated in RAPD reaction by using 20 primers screened from 80 primers, of which 110 were polymorphic, accounting for 66.67%. At species level, Neis gene diversity index (H), Shannons information index (I) and genetic differentiation coefficient (Gst) were 0.220 5, 0.304 7 and 0.908 2, respectively. P. hendersonii germplasm resources share a high level of genetic diversity, and genetic differentiation mainly exists among the populations. Results from genetic distances and cluster analysis showed that relationships among P. hendersonii populations were to some extent related with their geographical and climatic characters. [Conclusion] This study suggests that the conservation of P. hendersonii should focus on the protection of many populations, particularly the Qinghai population.