Gentiana sect. Cruciata is mainly found on alpine mountains across Eurasia, with the greatest species diversity occurring on the Qinghai-Tibetan Plateau (QTP). In this study, we determined the phylogenetic relationships between species within the Cruciata section to further elucidate the biogeographical processes governing these relationships. Phylogenetic reconstructions, based on both parsimony and Bayesian methods, were applied to data from four cpDNA fragments (>3,000 bp) that were obtained for 39 accessions belonging to Cruciata and related sections or outgroups. Our results suggested that all the species sampled within this section comprise a monophyletic group, but rejected all previous hypotheses regarding intra-sectional classifications based on gross morphology. Five clades were identified. The basal clade comprised three species that were endemic to the QTP. The clade that diverged second comprised three Central Asian species. The European clade, containing only G. cruciata, was grouped with the remaining two clades containing species from the QTP and central Asia. The biogeographic analyses and divergence estimates Suggested that this section diversified initially on the QTP within four million years. Given the low genetic differentiation, most species/clades may be the result of more recent differentiation. These results together confirmed the long-standing hypothesis that alpine plants in Central Asia and Europe originated from the QTP and/or West China and diversified extensively after the Pliocene when global temperatures decreased.