In this study, we investigated the population genetic structure and evolutionary history of Pinus armandii and we aim to speculate the refugia of this species during Quaternary ice ages. The bipaternallyinherited nuclear gene AGP6 was utilized to study the genetic variations within and among 27 natural populations (129 individuals) of P. armandii in China. The results showed that：(1)P. armandii have a higher level of nucleotide diversity (π_t= 0.013 8, π_sil= 0.030 6) than the other Pinus species.(2) Bayesian clustering divided the total samples into two groups: one was from the middleeastern region and another was the southwestern group in China. Both the Network and phylogenetic analyses supported this conclusion. (3)Analysis of molecular variance (AMOVA) showed that the genetic variation mainly occurred within populations (65.65%) and among groups (30.18%), and only a little genetic variation occurred among populations (4.17%). A strongly multimodal mismatch distribution curve indicated that no recently population expansion took place for this endemic species.(4)Based on the geographic distributions and genetic diversity patterns of AGP6 haplotype, we speculated that P. armandii had several refugia in the Qinling Mountain and the Hengduan Mountain areas. The longtime geographic isolation between different refugium areas and heterogeneous habitats induced by large mountains and rivers may have resulted in the high level of population differentiation. In addition, the distinctly population genetic structure and evolutionary dynamics could be another contributing factor to the high level of nucleotide diversity of P. armandii.