Abstract: The Hengduan Mountains are a global biodiversity center and hotspot of plant evolution research. Being endemic to the Hengduan Mountains, Gentiana hexaphylla Maximowicz ex Kusnezow shows continuous morphological characters with many of its closely related species. In this study, 21 populations were sampled to distinguish the G. hexaphylla complex through key morphological characters at the population level, and to explore genetic divergence and demographic history based on one chloroplast fragment. The number of haplotypes, average haplotype diversity, nucleotide diversity, and genetic diversity index(Pi) were 0.444, 0.00732, and 3.73, respectively, indicating high genetic diversity in the complex. Haplotypes were rarely shared among populations and most genetic variation occurred among populations (72.74%) rather than within populations (27.26%). Bayesian analysis indicated that genetic divergence in the complex occurred within the last two million years. Mismatch distribution and neutrality tests consistently showed that the G. hexaphylla complex has not experienced significant population expansion recently. In conclusion, genetic divergence within the G. hexaphylla complex has been shaped by climatic and environmental changes during the Quaternary as well as by geological isolation in the Hengduan Mountains.