Abstract: The genetic diversity of different natural Pinus sylvestris var. mongolica populations was analyzed along four altitude grades, three community types and three latitude grades by using ISSR DNA technique. Sixteen arbitrary primers were selected in the amplification, 162,156 and 169 polymorphic loci were produced in three groups with 240 sampled individuals. The total percentages of polymorphic loci reached 85.26%, 82.11% and 88.95% in three groups, which indicated the higher genetic diversity of natural P.sylvestris var. mongolica populations in the study area. Along the altitude, community and latitude factors, the genetic variations among the populations were relatively low. The genetic variations were mainly occurred within P.sylvestris var. mongolica populations. Genetic diversity of P.sylvestris var. mongolica was notably affected by the altitude and latitude, and little influenced by the community types in the study area.