| Pinus bungeana belonging to the Pinaceae, is the only three-needle pine of East Asian, and an endemic species of China, get a special status. It is of economic and ornamental value. Historical reasons, logging, and physical characteristics lead to sharp decline in current distribution area, and now Pinus bungeana has only small and sparsely distributed populations with limited individual numbers. We are get to study the genetic distribution pattern of pinus bungeana and the reasons, and explore the refugia of the quaternary glacial period and the later migration routes.We chose the chloroplast DNA trnD-T for sequencing 200 individuals from 20 natural populations. The results showed that there were 4 variation sites and 5 hplotypes in trnD-T gene. Total gene variability Ht=0.437 is larger than gene diversity with populations Hs=0.172. Genetic differentiaiton indicated no significant phylogeographic structure(Gst= 0.59397, Nst= 0.58914, P>0.001). SAMOVA divided the 20 populations to three groups, which was similar to the geographical distribution pattens of haplotypes(K=3, Fct=0.73366):1. Qinling southwest area; 2. LvLiang mountains southern region; 3. The area between Qingling and LvLiang mountains. The ancient haplotypes mainly distributed in the first two areas, where high levels of haplotype diversity were found, and they could be speculated as glacial refugia. Post-glacial expansion was supported by mismatch analysis. During the migration process H1 replaced of H4 as the current dominant haplotype. Populations from South Qinling had little been affected because of the limitation of pollen transmission.
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