Abstract: The Qinghai-Tibet Plateau（QTP）is one hotspot of studies about biodiversity,speciation and adaptive evolution.Gentiana algida var.purdomii,belonging to Gentianaceae,is endemic to the QTP and has high value in medicine.Based on populations across the QTP,we assessed its genetic structure,divergence and demographic history based on plastid and nuclear DNA sequences in this study.Palaeo-distribution was also reconstructed by species distribution model.High level of genetic diversity was observed in G.algida var.purdomii.Genetic differentiation was high in plastid data（FST=0.452）but low in ITS data（FST=0.022）,indicating high level of gene flow in G.algida var.purdomii.Neutrality test and mismatch distribution analysis both showed signatures of recent population expansion.Species distribution modelling showed slight range expansion from the Last Glacial Maximum to the present day.Divergence time estimates suggested that the onset of intraspecific diversification generally fell into the Quaternary.The results indicated that the intraspecific divergence in G.algida var.purdomii should be related to geographical isolation and range fragmentation in glaciations.This study provides insights into genetic differentiation,adaptive evolution and conversation in Gentiana as well as alpine plants in the QTP.