Abstract: Rapid global climate change profoundly affects species adaptation and biodiversity. As a relict tree species, Ginkgo biloba faces severe challenges in adapting to these changing conditions. Consequently, elucidating its adaptive potential to future climates is essential for formulating targeted conservation strategies. We selected 14 ginkgo populations with relatively uniform genetic backgrounds for population genetic and landscape genomic analyses. These populations were classified into five genetic subpopulations (G1–G5). Notably, the Funiu Mountain population, representing the sole member of subpopulation G3, exhibited unique genetic characteristics, including distinct differentiation, low diversity, and high heterozygosity. This pattern suggests that severe historical bottlenecks, small effective population size, founder effects, or prolonged geographic isolation may have shaped its genetic structure. Using latent factor mixed models, we identified 52 135 environmentally adaptive loci. Redundancy analysis indicated that environmental factors explained a greater proportion of both adaptive (22.8%) and genome-wide (11.1%) genetic variation than geographic factors (14.5% and 5.9%, respectively). Furthermore, adaptive genetic variation among subpopulations was driven by distinct environmental factors. Gradient forest analysis revealed that temperature-related variables (bio3, bio6, and bio7) and altitude were the primary drivers of adaptive genetic variation in ginkgo. Critical thresholds for shifts in adaptive variation were identified, including an altitude of 300 m and precipitation of coldest quarter of 135 mm. Projections of genetic offset under future climate scenarios indicated that ginkgo would face increased genomic vulnerability and a higher risk of non-adaptedness under high carbon emission scenarios, particularly for populations in the Qinling‑Huaihe region, Sichuan Basin, and Nanling Mountains.

Key words: Ginkgo biloba, Landscape genomics, Local adaptation, Genomic vulnerability