The Kunming-Montreal Global Biodiversity Framework recognised the urgency of taking action to conserve intraspecific genetic diversity (IGD) as an insurance against habitat degradation and environmental change. Recent work suggests that 90-99% of IGD should be conserved to safeguard viability of future generations.Here, we addressed such conservation issue in three forest tree species in Italy: silver fir (Abies albaMill.), Heldreich’s pine (Pinus heldreichiiH. Christ), and pedunculate oak (Quercus roburL.). We used microsatellite markers to measure IGD of 36 (A. alba), 15 (P. heldreichii) and 25 (Q. robur) natural sites, including several putative glacial refugia. We developed a Spatial Conservation Prioritisation (SCP) analysis to quantify the genetic irreplaceability of each site and identify the minimum set coverage ensuring IGD protection. Finally, we compared SCP results with the contributions to diversity within and between sites, total allelic richness and private allelic richness.We found that between 44% and 73% of sites were required to conserve 90-99% of the alleles, and that this conservation effort held even when targeting lower percentages of alleles to protect (50-75%). Glacial refugia were often included in the minimum set coverage, confirming theoretical and biogeographical expectations. Finally, sites with high genetic irreplaceability were found to have higher private allelic richness on average. These results are discussed in the light of the biogeographic history of the species studied and the current policies for the conservation of forest genetic resources.