Abstract: Nowadays, the genetic improvement of Pinus sylvestris var. mongolica is in a critical period of upgrading and updating. But the frequent allocation and exchange of breeding resources in different areas lead to unclear information of breeding resources and confusion of genetic relationship, which increases the risk of inbreeding depression during genetic improvement of Pinus sylvestris var. mongolica. Therefore, the evaluation of breeding resources is an important basis for the utilization of superior individuals of Pinus sylvestris var. mongolica. In this paper, 224 clones of Pinus sylvestris var. mongolica from the 1st, 1.5th and 2nd seed orchards were studied. Genetic diversity, phylogenetic relationship and genetic diversity were analyzed based on SSR, and the population of BaogenYuan and Yulin was relatively low according to breeding resource analysis; the genetic diversity of four populations of LiangZhongJiDi, TouDaoQiao, YuLin1.5 and TaiLai was higher.According to improved generation analysis, different generations of Pinus sylvestris var. mongolica breeding resources maintained a high level of genetic diversity; the genetic diversity of the high generation seed orchard decreased, and the expected heterozygosity (He) of the 2nd and 1.5th generation seed orchards decreased by 4.13% and 1.31% respectively compared with the 1st generation seed orchard; the 2nd generation seed orchard group had more higher inbreeding coefficient (the F-value was 0.173) and homozygote, which significantly deviated from Hardy-Weinberg equilibrium; Pinus sylvestris var. mongolica breeding resources in different habitats and the same source had no obvious variation, the genetic variation mainly existed among individuals (96%); with the generation seed orchard increased, phylogenetic relationship clustering phenomenon among clones gradually became obvious, two sets of breeding resource clones were identified completely genetic consistent in the 2nd generation seed orchard. The results of this research improve the breeding resource evaluation system of Pinus sylvestris var. mongolica, determine the genetic relationship of different generation breeding resources, and provide the material and information basis for the advanced genetic improvement work of Pinus sylvestris var. mongolica.