Effective conservation actions for endangered species rely on a good understanding of the evolutionary forces driving population decline. Detailed genetic analyses, including assessment of demographic history, population structure and diversity, are essential for gaining insights into the species’ adaptive potential and developing strategies of genetic rescue. Salix baileyi is an endemic vulnerable species in China with extremely small population sizes and a limited distribution. The samples of S. baileyi used for whole-genome resequencing cover its whole distribution. The results reveal four distinct genetic lineages within S. baileyi (DBSW, DBSE, TMS, and LXS), with divergence likely driven by paleoclimatic events and geographic barriers. All populations contracted during the Marine Isotope Stage 5 (MIS 5) up to the Last Glacial Maximum (LGM), with most recovering after the LGM, except for LXS lineage that continued to decline. Our results show that climate events, isolation barriers, inbreeding, and population bottlenecks have impacted the genetic status and evolutionary potential of these lineages of S. baileyi. Lineage-specific conservation measures should be applied based on the unique population dynamics of each lineage. This study provides valuable results for studies of vulnerable dioecious plants.