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With climatic change and anthropogenic activities, endangered species in subtropical China face high risk of extinction. However, many of them have received little attention in the past. In this study, three chloroplast DNA fragments (trnL-trnF, trnH-psbA, rps16) and integrated species distribution models were employed to evaluate the genetic diversity, genetic structure and distribution area changes of the endangered tree species Diplopanax stachyanthus. We identified three lineages (i.e., the eastern, central and western lineages) and high levels of genetic diversity in this species. The genetic differentiation is extremely high among the three lineages and among populations; most of the ten populations fixed private haplotype(s). Our time estimation elucidated that the splits of these lineages occurred during Pliocene to Pleistocene. Bayesian skyline plots analyses showed the change of effective population size of D. stachyanthus at ca. 0.1Ma. Multiple interglacial refugia were inferred for D. stachyanthus in subtropical China. Climatic fluctuation and geographic changes during the Quaternary as well as habitat losses may have played important roles in driving intraspecific divergence and shaped current genetic structure of D. stachyanthus. Furthermore, there may be a major decrease in the suitable habitats for this species. Our findings would shed light on the evolutionary history of D. stachyanthus in subtropical China, and facilitate the conservation and management of this species.