In order to explore the genetic structure differences of natural populations of Pinus bungeana in geographical distributions. Genetic structure of 5 distribution regions was studied using 7 pairs of SSR primes. The result showed that: 14 polymorphic loci were detected in 476 individuals among five regions. The observed number of alleles（Na）, effective number of alleles (Ne), Shannon's information index (I), observed heterozygosity (Ho), expected heterozygosity (He) and Nei's expected heterozygosity (Nei's) were 1.7143~2.1429、1.1942~1.571、0.1948~0.4954、0.1726~0.3116、0.1178~0.3325、0.1172~0.3307 respectively. The genetic diversity was relatively low among regions but the difference was high. The regions with the highest genetic diversity were west side of the Qinling Mountain followed by the Daba Mountain; the Taihang and Lvliang Mountain were relatively low. Genetic differentiation coefficient (Fst) was between 0.0138 ~ 0.2242 and gene flow (Nm) was between 0.865 ~ 17.8646 among regions. The populations with high genetic differentiation and gene flow were west side of the Qinling Mountain and among the regions of west side of the Qinling Mountain and other regions. Genetic diversity center of Pinus Bungeana were mainly distributed in the west side of the Qinling and Daba Mountain, therefore, the protection of Pinus Bungeana shoud focus on these regions.