BACKGROUND/OBJECTIVES: The stone pine (Pinus pinea L.) is an evergreen coniferous species valued for its edible seeds, which provide significant economic benefits to local populations. Remarkable phenotypic plasticity but low genetic variation characterizes the species. In Greece, natural populations of P. pinea are part of the Natura 2000 network and are protected under Annex I Priority Habitat type 2270. These populations, located across six Natura 2000 sites (including two islands), face increasing threats from tourism and climate change, leading to ecosystem degradation. Genetic and epigenetic studies are critical for the conservation of forest species because they provide insights into the genetic diversity, adaptive potential, and resilience of species, helping to inform effective management strategies and protect biodiversity in changing environments. This study aims to assess the genetic and epigenetic diversity of P. pinea in four Natura 2000 sites using molecular markers and to propose conservation strategies to ensure the species' long-term sustainability. Additionally, a preliminary investigation of water potential under maximum daily water demand was conducted to evaluate the species' adaptive response. METHODS: Genetic analysis was performed using Amplified Fragment Length Polymorphism (AFLP) markers, while epigenetic analysis was conducted using Methylation-Susceptible Amplified Polymorphism (MSAP) markers. Sampling was carried out in four Natura 2000 areas, where genetic and epigenetic diversity patterns were examined. Furthermore, a preliminary study on water potential under peak daily water demand conditions was conducted to assess the species' physiological adaptation to environmental stress. RESULTS: The results of this study provide valuable insights into conservation strategies by highlighting the potential role of epigenetic variation in the adaptability of P. pinea, despite its low genetic variability. Understanding the species' epigenetic flexibility can inform conservation efforts aimed at enhancing its resilience to environmental stressors, such as climate change. Additionally, the preliminary water potential analysis contributes to identifying physiological traits that may help predict the species' survival under varying environmental conditions, guiding the development of more targeted conservation practices and management plans. Further research could refine these findings and strengthen their application in conservation efforts. CONCLUSIONS: The conclusions emphasize the critical importance of this research in informing conservation efforts for P. pinea in Greece, particularly considering climate change and human pressures. The results highlight the need for both in-situ and ex-situ conservation strategies to ensure the long-term sustainability of the species. The key recommendations include the protection of natural habitats, the implementation of controlled seed collection practices, and further research into the epigenetic mechanisms that may enhance the species' resilience to environmental stress. Future studies should focus on deepening our understanding of these epigenetic factors and their role in the adaptability of P. pinea, which will be essential for developing more effective conservation measures.