To estimate the genetic diversity of Hippophae rhamnoides ssp. Sinensis-Frankia from root nodules, PCR-RFLP molecular marker was employed to compare 106 nodule samples of H. rhamnoides ssp. Sinensis individuals collected at seventeen sites from Kulun of Inner Mongolia to Xining of Qinghai Province, China. The PCR products of nifD-nifK intergenic spacer (IGS) were digested with HinfⅠ、HaeⅢand MboⅠ. 21 discernible loci are obtained from 106 samples, and 80.99% are polymorphic of these loci (PPL=80.99%). All samples are divided into 9 IGS types. Dendrogram analysis indicates the rich genetic diversity of Frankia from H. rhamnoides root nodules. The richness of genetic diversity in good soils is greater than in bad soils, and greater in high evelation regions than in low evelation regions. At least 2 genotypes are found at most sites. The genetic distances among different genotypes vary 4.88%-55.96%, their distribution is nonhomogeneous, and the phylogenetic relationship among different Frankia genotypes is not found to correlate with sites. Frankia in nodules of Hippophae rhamnoides ssp. Sinensis can be divided into two genotype groups. The genotypic distribution in groups is relatively consistent, while the genotypic distribution between groups is obviously different.