Amygdalus mongolica is a Tertiary relict plants widely distributed on the arid region of Northwest China, noncoding chloroplast DNA was amplified and sequenced in 324 individuals from 17 populations sampled from the entire distribution range of A.mongolica. The main results are as follows: (1) the length of trnHpsbA sequence was 350 bp, a total of 63 polymorphic sites were identified and 9 haplotypes were recovered. Total genetic diversity was 0.758, average genetic diversity within populations was 0.203. Populations from the Helan Mountains and southern foot of Yin Mountain owned high haplotype diversity and nucleotide diversity and fixed more private haplotypes, which suggested that the eastern margin of the Helan Mountains and southern foot of Yin Mountain were important refugium during the Quaternary glaciation. (2) AMOVA analysis suggest that 83.84% of total variation existed among populations and 16.16% existed within population, there is no significant phylogeographic structure (N_st=0.733, G_st=0.655, P>0.05). The natural populations of A.mongolica could be divided into eastern group and western group based on the geographical distribution and network of haplotypes, there were no shared cpDNA haplotypes between the two groups. The high level of genetic differentiation and genetic diversity were found based on the population genetic analysis, and no significant phylogeography was existed in the populations of A.mongolica. (3) The populations of A.mongolica have occurred the expansion events during the interglacial periods or postglacial. Founder effect occurred during the population expansion which lead to only one haplotype in the most populations.