In order to provide theoretical support for reasonable protection and utilization of Siberian apricot resources, we analyzed the genetic diversity and population structure of 13 Siberian apricot populations in Inner Mongolia through twentyseven pairs of SSR markers. The results showed that: (1) a total of 512 alleles (N_a) were identified based on 27 SSR molecular markers, the average number of alleles (Na) per locus and polymorphism information content (PIC) per locus were 19 and 0.84, respectively. A high level of genetic diversity was revealed by Shannons information index (I, 2.25) and expected heterozygosity (H_e, 0.73) 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 6.95, 4.48, 1.60, 0.76 and 0.56, respectively at population level. Comprehensive analysis suggested that Kezuohouqi population exhibits the highest level of genetic diversity, whereas the population of Keshiketengqi exhibits the lowest level of genetic diversity. (3) The genetic differentiation coefficient (F_st) based on Fstatistic and gene flow (N_m) were 0.12 and 1.86, respectively; Analysis of molecular variance showed that the most of the genetic variation within population (92%), more than that among populations (8%). (4) The genetic distance among populations in Inner Mongolia Siberian apricot ranged from 0.04 to 0.67, the genetic identity among populations in Inner Mongolia Siberian apricot ranged from 0.33 to 0.83. UPGMA cluster analysis, principal coordinates analysis (PCoA) and structure analysis showed that 13 populations could be divided into four clusters. The Mantel test showed that the genetic distance among the populations was significantly correlated with geographic distance (r=0.453, P< 0.01). All the results supported that the genetic diversity of Siberian apricot in Inner Mongolia was relatively abundant, which was related to its size of population, long historical evolution and biological characteristics. There was a moderate genetic differentiation among populations, which resulted from the geographical isolation and fragmented environments caused by current human influences.