Genomic DNA of 240 plant samples from eight populations of Potaninia mongolica Maxim. in China was amplified with 8 pairs of primer to evaluate the population genetic diversity of this endangered species by using amplified fragment length polymorphism (AFLP) analysis. 397 clear bands from 65 to 530bp were available for analysis and 296 (74.56%) of them were polymorphic. So it amplified 37 polymorphic bands for each pair of AFLP primer. PopGen32 data processing software gave out that Nei′s gene diversity index ranged from 0.0845 to 0.1779 and Shannon′s information index ranged from 0.1280 to 0.2377 for the 8 populations, among them the highest population genetic diversity level was in Shangshawo which will be one of the germplasm centers and the lowest of it was in Yingen. The analysis of variance showed that the variance between populations was 31.69% and the main variance was 68.31% within populations, the UPGMA cluster analysis showed that the mean genetic distance among the 8 populations was 0.1341. the UPGMA cluster analysis results also revealed that the population genetic diversity of P. mongolica Maxim was closely related to its distribution area and had high genetic similarity between the populations. This conclusion implied that population of P. mongolica Maxim. had same origin and genetic drift was of no importance for its diversity. The research suggest that the best way for ex situ conservation was collecting sufficient individual plant from as many populations as possible and bring the full effort to keep the genetic diversity of it, because this is the basis for the study of systematic evolvement of P. mongolica Maxim.