Munronia delavayi Franch. (Meliaceae) is a vulnerable perennial species that is narrowly distributed and endemic to the dry-hot valley of the middle/lower Jinsha River. However, 12 hydropower stations are currently scheduled to be built in the middle and lower Jinsha River drainage and their distribution overlaps with the range of M. delavayi. The construction of these hydropower stations will cause flooding of the adjacent habitats that support M. delavayi and will change the local ecological environment, which may result in a new and dangerous situation for the survival of this species. Our aim was to evaluate the population structure and propose the most suitable conservation strategy for M. delavayi to support its adaptive potential. In this study, we collected 70 individuals from seven populations that covered most of the geographic range along the Jinsha River and investigated the population diversity, genetic structure and demographic history of this species by analyzing the variations in one mitochondrial marker (18sf-5sr), two non-coding chloroplast DNA regions (trnT-trnL, trnS-trnG), and one nuclear DNA marker (Gs687f-994r). As a result, three mitotypes, nine chlorotypes and six haplotypes with high genetic diversity (H-T = 0.580, 0.774 and 0.740) were detected based on mtDNA, cpDNA and nDNA and a strong genetic structure (F-ST = 0.855 and 0.545) was detected based on cpDNA and nDNA. Our study also indicated that habitat fragmentation and limited gene flow may result in the genetic differentiation of this species and that the population distributed in Qiaojia, Yongshan and Panzhihua should be proactively protected based on the conservation genetic analysis.