Population genomics of Quercus gilva provides insights into the conservation of fengshui forests.

Human-driven environmental changes threaten the region's dominant trees. China's fengshui forests harbor ancient trees with cultural and ecological significance, yet their climate resilience remains uncertain. By integrating genome and resequencing data, we investigate the structural variants, demographic dynamics, and local adaptation of Q. gilva, a threatened East Asian oak vital to fengshui traditions. The genome structural variants are enriched in critical pathways such as stress response and genome maintenance. Divergence of Q. gilva populations into Chinese and Japanese lineages occurs during mid-Pliocene climatic shifts. The Chinese lineage carries a higher genetic load, including deleterious mutations in histone deacetylase-associated genes that may impair adaptability. We propose four populations (Changning, Kiyosumi, Tama, and Lianyuan) as preliminary conservation priorities due to their higher genetic diversity and lower genetic load. In contrast, the Jianou population, which contains at least 240 ancient trees, may be susceptible to inbreeding depression as a result of its low genetic diversity and high genetic load. However, enhancing population resilience to future climate change through genetic rescue will depend on further comprehensive genetic and ecological studies.