Climatic oscillations during the last glacial maximum (LGM) have played important roles in the distributions and genetic structures of extant species. Here, we investigated the population structure of a deciduous shrub species, Rhododendron dauricum L., across its current geographic distribution in northeastern China based on six chloroplast regions (trnS-trnfM, trnL-ndhJ, rpoC1-rpoB, trnS-trnG, trnH-psbA, and trnK-matK). A total of 11 haplotypes were identified. The results showed a significant geographic distribution pattern (N_ST > G_ST p < 0.01) in northeastern China. In addition, our results showed that there were high levels of genetic diversity in R. dauricum and that more than 70% of the genetic variability was distributed among groups. Furthermore, results from the neutrality test failed to identify population expansion at the whole-species level. These findings together suggested that R. dauricum shows spatial genetic structure and that the LGM has had profound impacts on the geographic distribution and genetic variability of this species.