is an endangered officinal herb distributed in the Tianshan Mountains of northwestern China. We examined its phylogeography to study evolutionary processes and suggest implications for conservation. Six haplotypes were detected based on three chloroplast non-coding spacers (psbA-trnH, rps16, and trnS-trnG); genetic variation mainly occurred among populations and SAMOVA groups. This species is distributed in different deep valleys, and we speculate that these fragmented habitats cause gene flow barriers among populations and groups. We also speculate that during glacial periods, extremely low temperatures and aridity caused additional range shrinkage and fragmentation, factors consequently resulting in significant intraspecific differentiation in allopatric regions. For setting a conservation management plan, we identified the Lucaogou region as the most important area, and we designated two ESUs for separate management.