In order to study the origin of common apricot and the phylogenetic relationship of different cultivars group, phylogenetic tree and median-joining network of chloroplast haplotypes were analyzed by using 9 cpSSR primers to detected 58 materials from 9 cultivars groups and used 3 Prunus mume as control. The 22 alleles consisted of 15 haplotypes in 61 materials. H01 (haplotype 01), H02 and H03 which had higher frequency in common apricot were 3 dominant haplotypes. Most of the cultivars groups had dominant haplotypes except for South China cultivars group. The common apricot in Northwest had only 3 dominant haplotypes, while the wild common apricot in the Ili River valley in Xinjiang had only 2 dominant haplotypes but no other haplotype. At the same time, the number of haplotypes detected in the Northeast cultivars group, the South China cultivars group and the Southwest local cultivers were more than that of the main producing areas. The phylogenetic tree of 15 haplotypes showed that all common apricot haplotypes were clustered into 2 major branches. The first branch is based on H01 and H03, while the second branch is based on H02. The dominant haplotypes H01 and H02 were in the center of the median-joining network. The evolution of common apricot chloroplast genome was obviously conserved and there were a few mutations in the chloroplast genome. In the spreading process of the common apricot, the germplasm resource in cultivars groups distant from the center of origin such as South China, Northeast and Southwest cultivars groups had more introgression in chloroplast genome and there were more adaptable mutations in their chloroplast genome.