In order to investigate the genetic structure and historical dynamics of natural populations of Xanthopappus subacaulis， we sequenced the DNAs of 147 individuals from 49 populations based on ten single-copy nuclear genes. Multiple methods， including STRUCTURE clustering and molecular variance analysis， were employed for analysis. The results indicated that the polymorphic loci of X. subacaulis ranged from 3 to 11， with haplotype diversity index （H_d） ranging from 0.558 to 0.883， nucleotide diversity index （π） from 0.001 32 to 0.006 03， and mean nucleotide differences （K） from 0.738 to 3.325， indicating rich genetic diversity. The tested populations of X. subacaulis could be divided into two major genealogical branches in the north and south， with 83.04% of the genetic variation among populations and only 16.96% within populations. The degree of genetic differentiation was high （F_ST=0.830， P<0.01）， and gene flow was extremely low （Nm=0.112）. The genetic distance was significantly positively correlated with the geographical distance （r=0.537，P<0.01）. The divergence time of the two major genealogical branches was approximately 3.33 million years ago， which was related to the uplift of the Qinghai-Xizang Plateau and the climate change during the Quaternary glacial period. Moreover， there was no recent population expansion. This study revealed the influence of geographical isolation， climate differences， and historical events on the genetic structure of X. subacaulis， which provided important data for its conservation of germplasm resources and adaptive evolution research.

Single copy nuclear gene  /  Xanthopappus subacaulis  /  Genetic diversity  /  Genetic structure  /  Geographic isolation