Abstract: SSR markers were used to describe the genetic diversity and population structure of 220 elite genotypes in five populations of Larix principis-rupprechtii Mayr plantation in Beijing. A total of 81 alleles were amplified using 20 SSR markers while 4.05 alleles were detected on average per locus with the range of 2-8. The means of observed and expected heterozygosities were 0.429 and 0.440, respectively. Shannon's information index and Polymorphic information content for these populations were 0.756 and 0.380, respectively. Among the five populations, BHS and YMS populations had the highest level of genetic diversity, while WLS populations had the lowest one. The analysis of molecular variance exhibited that 2.65% of genetic variation was observed among populations, while the remaining 97.35% of genetic variation was within the populations. The coefficient of genetic differentiation was only 0.023, elucidating that the extent of genetic differentiation was quite low. The five populations could be divided into three groups based on the Nei’s genetic distances between populations, group Ⅰincluded SH and WLS, group Ⅱ included SS, and group Ⅲ contained BHS and YMS. The result of population structure analysis based on STRUCTURE software was roughly consistent with cluster analysis. The results of this study will provide the theoretical foundation for the collection, conservation and utilization of excellent germplasm resources and evaluation of genetic diversity in the man-made forest.