Genetic diversity is important for the long-term survival of species and plays a critical role in their conservation. To manifest the adaptive potential, it is necessary to preserve the allelic diversity of populations, including both typical and region-specific alleles. Molecular genetic analysis of 22 populations of Scotch pine (Pinus sylvestris L.; Pinaceae) in 10 subjects of the Russian Federation in the East European Plain and the Middle Urals was carried out. Molecular genetic analysis of 22 populations of P. sylvestris revealed 182 polymorphic PCR fragments. The studied populations are characterized by a medium level of genetic diversity. A high subdivision coefficient (GST) of the studied populations was established, the intensity was 0.559. At the same time, the level of sub-division differed for different regions, for the populations from the Middle Urals it was 15.5% (GST = 0.155), and for the populations from the East European Plain, it was 55.8% (GST = 0.558). The dendrogram of genetic similarity shows 5 clusters of the studied populations of P. sylvestris according to their geographical location. The populations from the East European Plain are mostly characterized by typicality, while the populations from the Middle Urals, on the contrary, are more specific in gene pools. The use of the coefficient of genetic originality to identify populations with typical and specific alleles allows for solving the problem of selecting populations for the conservation of forest genetic resources. The data obtained on genetic diversity, and the structure of populations growing in areas of active logging, are important for determining the geographical origin of plant samples; which is an integral part of the control of illegal logging.