The cytogenetic analysis of the Pinus sylvestris L. seed progeny in the forests of the northern taiga in the Far North of Russia conditions was carried out. Two Pinus sylvestris populations growing in Ambarnskoy and Pyaozerskoy forest divisions of Loukhsky district of Karelia Republic were studied. The number of chromosomes, the frequency and types of mitosis disturbances at the metaphase, anaphase and telophase (as a percentage of the total number of dividing cells at the same stages), and the frequency of micronuclei occurrence, as well as the laboratory seed germination, were studied. As a result of the study, it was found that 50–56% of the studied sprouts were mixoploid. Analysis of mitosis showed that the root meristem of the studied samples contained cells with various pathologies; simultaneously, the frequency of mitosis pathologies in the Ambarnskoy population was significantly higher than in the Pyaozerskoy one. It amounted to 6.8 ± 0.4 and 4.9 ± 0.4%, respectively. Nine types of abnormalities were identified; chromosome overrun and bridges prevailed. Micronuclei were registered in 35–38% of the studied Pinus sylvestris sprouts. At the same time, the proportion of cells with micronuclei in the Ambarnskoy population was 2-fold higher than in the Pyaozerskoy one and averaged 0.12 ± 0.03% and 0.07 ± 0.02%, respectively.