In this work, based on the results of the microsatellite loci (PtTX2123, PtTX2146, Spac11.8) tests, we provided a comparative evaluation of the genetic structures and levels of genetic diversity of the following populations: two plus stands from Velikaya Guba and Zaozerye, four natural populations from Vodlozero, Zaonezye, Kivach, Sortavala, and a clonal seed orchard of Scots pine. Unlike the natural populations, which were represented by intact rocky pine forests growing on relatively poor soils, the plus stands were represented by secondary v. myrtillus forest stands formed on relatively fertile soils. Amplification of the microsatellite loci of the studied populations and the seed orchard of Scotch pine helped to identify 32 alleles in total. Overall, the allelic diversity of the plus stands proved to be close to the mean value for the studied populations. The tested natural populations, plus stands, and the seed orchard of Scots pine are characterized by different levels of genetic variability. The plus stands, featuring better growing conditions in comparison with the natural populations, demonstrated an intermediate level of genetic diversity. However, the differences between them and the natural populations were statistically unreliable, and the only statistically significant parameter was the Wright fixation index F. The maximum values of this index (0.142 and 0.106) indicate a significant deficit of heterozygotes in the Scots pine plus stands.