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Psathyrostachys huashanica Keng is endemic to China and only distributed in Huashan Mountain in Shaanxi Province, China. In this study, 15 P. huashanica populations consisting of 450 individuals sampled across their main distribution were investigated by using the simple sequence repeats (SSRs) markers. A total of 184 alleles were detected on 24 SSR loci, and the number of alleles on each locus ranged from 2 tol5, with an average of 7.667. The total gene diversity (HT= 0.683) and the coefficient of population differentiation (GST=0.125) showed that P. huashanica had a relatively high level of genetic variation, and the genetic variation was mainly distributed within the populations. The gene flow among the populations of P. huashanica (Nm= 1.750) was much less than that of the common anemophytes (Nm = 5.24). Correlation analysis demonstrated that the number of alleles as well as genetic diversity of the five populations of Huangpu valley decreased along with the increase of altitudes, but the correlation was not significant. Implications of these results for future P. huashanica collection, evaluation and conservation were discussed.