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Pleistocene climatic fluctuations have affected the evolution of the genetic structure of many organisms. In this study, we test the hypothesis that glacial-interglacial cycles are traceable from genetic footprints retained within plant species. Fourteen populations belonging to the Delphinium naviculare species group were sampled from the Tianshan Mountains in western China, and 14 genotypes were detected based on sequences of the two chloroplast fragments trnS-trnG and trnL-trnF. A Bayesian relaxed molecular clock approach revealed that genetic divergence in this species group began in the early Pleistocene and intensified during mid-Pleistocene. A lineage-through-time (LIT) plot shows dramatic accumulations of Delphinium lineages during the three Pleistocene interglacial periods in this area. From ecological niche modeling (ENM), it appears that the distribution of the species group most likely shrunk in the eastern and and southwestern high-altitude parts of its range during the Last Glacial Maximum (LGM), suggesting that cold and drought were primary drivers of lineage migration during glacial periods. Humid valleys at mid-elevation served as refugia at these times; however, during the latest two glacial epochs, new refugia likely appeared, corresponding to a decreased extent of glaciation. In accordance with the glacial chronology derived from many proxy data such as glacial tills, lacustrine sedimentary sequences, and oxygen isotope records, the genetic structure of the D. naviculare species group reveals a paleoclimatic history that is able to differentiate three glacial-interglacial cycles and an overall trend towards aridity during the course of the Pleistocene. (C) 2012 Elsevier B.V. All rights reserved.