The objective of this study is to contribute to the conservation of upland tree species in the face of climate change. We used a conservation index to prioritize the areas and populations of three conifer species in the mountains of Lebanon. This conservation index integrates (1) mountain topography to identify areas that could provide a suitable microclimate, (2) genetic diversity to assess the adaptive capacity of populations in these mountain areas, and (3) a hypothetical climate change scenario that could affect this Mediterranean region. The idea of this index is to prioritize protected areas based on a match between the relevance of the area to be protected and the populations that need local and long-term protection. The stronger the match, the higher the priority of the area to be protected. We applied this conservation index to 36 populations of 15 fir, 15 cedar, and 6 juniper. These populations were genotyped by different authors whose published data we used. The results show that 10 populations of the 3 species have a very high index and 9 others have a lower but still high index, indicating a high conservation priority. These 19 populations occur in 5 different areas that we delineated and that form a network along the Lebanon Mountains. We hypothesize that the conservation of these 19 populations across the Lebanon Mountains could contribute to the longterm sustainability of the 3 species in the face of a 2 °C increase in mean seasonal temperature and a 20% decrease in seasonal precipitation compared to the current climate.