Abstract:The genetic diversity of Oxytropis aciphylla Ledeb. was analyzed using inter simple sequence repeat(ISSR) markers. The results indicated that there was relatively high genetic diversity in Oxytropis aciphylla Ledeb. 215 bands were amplified from 5 natural populations by 11 ISSR primers. The percent of polymorphic loci was 98.14%. The Shannon information index I was 0.328 7, and Nei’s index H was 0.197 2.The total gene diversity Ht was 0.210 8, and the gene diversity within populations Hs was 0.160 4. 76.11% of genetic variation existed within populations while 23.89% of genetic variation existed among populations. The Gst was 0.238 9, and the gene flow was 1.592 9. There was genetic variation trend among populations. However the genetic drift would not cause the differentiation. The Nei’s UPGMA Dendrogram displayed that the genetic distance was close among 4 populations distributed in dessert steppe regions, while relatively far in a dessert population.