The genetic relationship of 10 M. ruthenica populations from Hebei, Liaoning, Jilin, Shanxi Provinces and Inner Mongolia and Tibet autonomous regions of China were analysis by AFLP. 8 primers with strong polymorphism and good repeatability were screened from 64 AFLP primers, generating a total of 640 bands of which 472 (73.8%) showed polymorphism. On average, the Nei’s gene diversity, Shannon’s information index and genetic similarity index (GS) were 0.157, 0.099 and 0.827, respectively. 10 M. ruthenica germplasms were divided into 3 groups with the higher correlation of geography resource by the cluster analysis and PC results. AFLP is the candidate molecular marker to reveal the genetic diversity of M. ruthenica. The results indicated that the wild population of M. ruthenica from the china had a rich genetic diversity in AFLP genotype and thus it was of great important to explore genetic evolution and gene resources and to preserve the local M. ruthenica populations in this area and expanded area.