In order to make clear the genetic background of Notopterygium forbesii,and provide theoretical basis for its protection,we assessed the genetic diversity and genetic structure of 138 individuals from 14 natural populations of N.forbesii,an endangered and endemic species in Qinghai,Gansu and Sichuan,using cpDNA trnS-trnG noncoding sequences.The results showed that:(1)Sequence length varied from 509 bp to 515bp and base composition was with high A+T content of 67.6%;(2)31 haplotypes were identified based on nucleotide variation.Among them,nine haplotypes(H5,H1,H9,H10,H16,H17,H19,H20,H22) were shared by different populations,and H5 was the most frequent haplotype and represented 48.56% of the total samples;(3)Relatively high level of haplotype diversity(Hd=0.750 3) and nucleotide diversity(Pi=0.007 11) were detected in 14 populations of N.forbesii.However,31 haplotypes from different populations mixed together and did not form distinct geographically separated clades.(4)Investigations of population differentiation(F_ST=0.602 4),gene flow(N_m=0.330) and AMOVA(60.24% genetic variation was partitioned among regions) all demonstrated that high genetic differentiation existed among population.(5)The genetic distance of 14 populations of N.forbesii ranged from 0.000～0.007,with an average of 0.003,indicating that the genetic relationship between populations of N.forbesii was relative far.And there was no significant correlation between genetic distance and geographic distance,illustrating that there was no obvious geographical trends of the distribution of the population genetic variation in N.forbesii.Many factors might attribute to the high level of genetic differentiation,such as:limited gene flow;genetic drift;geographical isolation.Based on our results,we proposed some conservation strategies.