In this study, we analyzed genetic diversity and population genetic structure of 8 natural distribution populations (total 105 individuals) based on ITS1ITS4 sequence of endangered plant Amygdalus pedunculata, to darify the geographical distribution and genetic diversity of A. pedunculata. The results showed that: (1) the length of ITS1ITS4 fragments is 583 bp; 13 variation sites and 8 haplotypes were obtained. Total genetic diversity was 0.727, average genetic diversity within populations was 0.564, haplotype diversity and nucleotide diversity ranged from 0.182 to 0.636 and 0.000 6 to 0.006 3, respectively; (2) Genetic differentiation among these populations was not very significant. AMOVA analysis show that 33.65％ of total variation occurred among populations and 66.35% occurred within population. Mean gene flow among the populations was 0.986. A significant phylogeography structure was observed (G_ST=0.225, N_ST=0.362, P＜0.05). Results of neutrality tests and mismatch distribution curves show that A. pedunculata did not experience recent population expansion. (3) Haplotypes of the MJ network and ML tree show that populations of Inner Mongolia and Shaanxi clustered into two genetic lineages.