Pine marshy forests Vaccinio uliginosi−Pinetum Kleist 1929 are associations included in Natura 2000 areas. They are at the highest risk of dismemberment due to global climate change. The study assessed the possibility of regeneration and genetic variability of Scots pine in a marshy forest habitat. The research was carried out in the Polesie National Park on the Durne Bagno and Lake Moszne peatbog. In the examined locations the phytocenosis of pine marshy forest was characterized. Subsequently the density of pine seedlings was estimated and their height measured. The genetic variability of the pine regeneration was estimated using the ISSR technique. Based on the research results, it was concluded that the regeneration potential of pine was low. On average, 200 regeneration plants were inventoried per hectare, and their average height was 26.34 cm. Significantly more pine regeneration was recorded (123 plants) in Lake Moszne, with an average height of 6.99 cm. By contrast, only 36 pine trees were inventoried in Durne Bagno, but their height was 45.69 cm. Scots pine genetic variability was similar in both locations. The percentage of polymorphic loci was 74.24. The average number of alleles per locus reached 1.685 and the effective number of alleles per locus was 1.405. The expected heterozygosity and Shannon index were 0.239 and 0.362, respectively. The phytocenosis was scarce, but characteristic of the Vaccinio uliginosi−Pinetum habitat. In total, 17 species were inventoried, of which 11 occurred in both locations. Light, humidity and habitat fertility indices were characteristic of this type of habitat and amounted to 6.98, 7.70 and 1.53, respectively. No relationship between undergrowth vegetation and the Scots pine regeneration was found. A negative effect of bog blueberry Vaccinium uliginosum L. on the number of pine regeneration was demonstrated only in the Durne Bagno location. Shading of the tree and shrub layer did not suppress the growth of Scots pine regeneration or undergrowth vegetation. Based on the study results, we concluded that the current state of preservation of pine marshy forests in the Polesie National Park was satisfactory. The presence of pine in the shrub layer allowed to conclude that the survival of seedlings in pine marshy forests was possible and could lead to their transition to the next developmental phases. However, as a result of the ongoing climate change and those predicted in the near future, we recommend constant monitoring of the habitat in order to maintain its sustainability.