A study of the biological properties of the Siberian pine (Pinus sibirica Du Tour) seeds was carried out. Four seed categories were used in the work, differing in size: large (11–14 mm in length), medium (9–10 mm), small (7–8 mm) and very small seeds (6 mm). The seeds quality study using the X-ray and the histochemical analyses showed that the size of the seeds can indicate their defectiveness. Fractions of small and very small seeds of Siberian pine turned out to be completely sterile, most of the seeds of large and medium fractions were viable. Cytoembryological studies have shown that in trees that form empty and underdeveloped seeds (fractions of medium and large seeds), disturbances in the embryological structures development can be observed. These disturbances take place at the stage of gametophytogenesis and the archegonia development. In trees with large seeds, gametogenesis proceeds without deviations, four archegonia are formed in the ovules, and polyembryonic seeds are formed (up to 16 embryos in the germinal canal). In Siberian pine trees with a one-year reproductive cycle, the seed size varies from very small to large. In these trees, the development of the female gametophyte is completed and archegonia are formed. However, in the ovules of trees with a one-year reproductive cycle, fertilization of eggs does not occur and seeds without an embryo are formed. During the period of stratification (four months), in most seeds of the medium and large fractions the intraseed, growth of the embryo was completely completed. In in vitro culture on MS medium with a low concentration of hormones, the growth of the germinal axis was carried out in seven days of cultivation. The embryos germinated successfully. Thus, based on experiments on the Siberian pine embryos cultivation, it can be concluded that the seeds of this species can enter organic (morphophysiological) dormancy. When creating optimal conditions for germination (nutrient substrat, temperature 24 ± 1°C), Siberian pine seeds are able to germinate.