Abstract: Carya kweichowensis is a critically endangered hickory species endemic to the karst forests of southwestern China. Its survival is threatened by severe habitat fragmentation and extremely small population sizes driven largely by human activities. In this study, we combined population genomic analyses with species distribution modeling to inform the conservation of C. kweichowensis. We sampled 66 individuals from 18 wild populations across its remaining range and generated genome-wide data for single-nucleotide polymorphisms to assess genetic structure, diversity, mutational load, and demographic history. The results revealed clear genetic subdivision of remnant populations into distinct groups corresponding to their geographic isolation. Demographic reconstructions suggested a history of population decline and bottlenecks, emphasizing the prolonged vulnerability of this species. Species distribution models predicted severe contraction and shift of its suitable habitat under future climate change scenarios, which would further imperil its persistence. Based on the genetic differentiation observed, we delineated three conservation units for C. kweichowensis. We recommend immediate conservation action for the marginal central and eastern groups. Our study demonstrates that the integration of population genomics, genetic load assessment, and species distribution modeling contributes profoundly to the development of targeted conservation strategies for endangered species.