The QinghaiTibetan Plateau (QTP) is one of the global biodiversity hotspots and renowned for its high level of endemics. Numerous studies have explored the genetic differentiation and evolutionary history of plants in this region, but the large number of Gentiana endemics have been overlooked. Focusing on an annual Gentiana species (G. haynaldii Kanitz) in the QTP, we assessed their genetic structure, divergence and demographic history based on plastid and nuclear DNA sequences in this study. The results showed that: (1) relatively high level of genetic diversity and differentiation was observed in G. haynaldii (cpDNA，F_ST=0.532； ITS，F_ST=0.511). Genetic variance nearly equally occurred among populations or within population. (2) Demographic analyses showed signatures of recent population expansion in G. haynaldii. Species distribution modelling showed stable potential range except slight range expansion from the midHolocene to the present day. (3) Divergence time estimates suggested that the onset of intraspecific diversification generally fell into the Late Pliocene and the Early Pleistocene. The results indicated that the intraspecific divergence in G. haynaldii should be driven by geographical isolation and range fragmentation in glaciations rather than orogeny. This study provides insights into genetic differentiation and evolutionary history of the speciesrich Gentiana as well as alpine plants in the QTP.