SSR (simple sequence repeat) markers were chosen for analyzing the genetic diversity and genetic structure of wild apricot, cultivation apricot by the capillary electrophoresis with fluorescence detection. The results were obtained as follows: Seventeen point eight two alleles (Na) and 7.44 effective alleles (Ne) per locus were identified using 27 SSR molecular markers; the average Shannon's information index (I), expected heterozygosity (He) and observed heterozygosity (Ho) were 2.23, 0.70 and 0.52, respectively. At the population levels, average number of alleles, effective number of alleles, expected heterozygosity, observed heterozygosity and Shannon's information index were 6.59, 4.15, 0.70, 0.53, and 1.50, respectively, which indicated that a high level of genetic diversity existed in apricot resources in China. The genetic diversity of wild apricot resources were significantly higher than cultivation apricot resources, the highest genetic diversity was Siberian apricot population that had the largest number of private alleles in wild apricot resources, however, the lowest genetic diversity was kernel-using apricot population, which had a few of private alleles in the cultivation apricot resources. The clustering result showed that 159 individuas could be divided into four clusters. Genetic structure analysis showed that 159 individuas divided into five groups, this result was line with the classification of the traditional morphology. At this present study, a high level of genetic diversity and complex population structure existed in apricot resources our country, wild common apricot germplasm and cultivation apricot had a close relatives and a similar genetic structure, it speculated that the wild common apricot was the original species of the cultivation apricot; on the contrary, the kernel-using apricot had a narrow genetic base, and had a low level of genetic diversity. These results also could provide important theoretical basis for the new variety breeding and sustainable utilization of apricot resources.