In order to provide theoretical support for reasonable protection and utilization of wild apricot, we analyzed the genetic diversity and genetic differentiation of four wild apricot populations from Xinjiang by using twentyseven pairs of SSR (simple sequence repeat) primers. The results showed that: (1) a total of 431 alleles (N_a) were identified based on 27 SSR molecular markers. The average number of alleles (N_a) per locus and polymorphism information content (PIC) per locus were 15.96 and 0.84, respectively. A high level of genetic diversity was revealed by Shannons information index (I, 2.21) and expected heterozygosity (H_e, 0.78) at species level. (2) The average number of alleles (N_a), number of effective alleles (N_e), Shannons information index (I), expected heterozygosity (H_e) and observed heterozygosity (H_o) were 10.98, 5.85, 1.92, 0.79 and 0.55, respectively at population level. Comprehensive analysis suggested that Xinyuanxian population exhibits the highest level of genetic diversity, whereas the population of Gongliuxian exhibits the lowest level of genetic diversity. (3) The genetic differentiation coefficient (F_st) based on Fstatistic and gene flow (N_m) were 0.05 and 5.26, respectively; Analysis of molecular variance showed that the most of the genetic variation within populations (95.4%), more than that among population (4.6%). (4) The genetic distance among population in Xinjiang wild apricot ranged from 0.06 to 0.49 with average of 0.24; the genetic identity among population in Xinjiang wild apricot ranged from 0.61 to 0.94 with average of 0.80. UPGMA cluster analysis and principal coordinates analysis (PCoA) showed that 4 populations could be divided into two clusters; The Mantel test showed that there was not a significant correlation between the genetic distance and geographic distance (r=0.332, P=0.16). All the results supported that the genetic diversity of wild apricot in Xinjiang was relatively abundant. Nevertheless, genetic differentiation and genetic distance was relatively lower, which resulted from the size of population, long historical evolution and frequent gene flow.