Catalpa huangxin, a distinctive taxon within the genus Catalpa in China, is valued for its ornamental beauty and durable yellow heartwood. However, its wild populations are declining due to climate change and human activities, posing urgent conservation challenges. The unclear genetic diversity and population structure further complicate its protection and breeding efforts. To address these issues, this study employed RAD-seq to analyze 198 samples, including 169 C. huangxin, 24 Catalpa duclouxii, and 5 Catalpa ovata (outgroup), focusing on phylogeny, genetic diversity, gene flow, and dispersal routes. The results show that C. huangxin and C. duclouxii are distinct but closely related taxa. C. huangxin was divided into five subgroups with moderate genetic diversity (He = 0.2935, Ho = 0.4401). Subgroup 5 exhibited the highest diversity, but significant genetic differentiation (F = 0.1983) was observed between subgroups, limiting gene flow and adaptation. Human activities, reproductive traits, and habitat fragmentation contribute to this differentiation. The study recommends in-situ conservation of genetically diverse subgroups, particularly Subgroup 5, artificial population restoration, germplasm banks, and expansion of its current distribution range. These strategies are essential for C. huangxin's protection and genetic improvement, offering valuable insights for the conservation of other species with similarly restricted distributions.