The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis, a dominant species of the conifer forests in the eastern declivity of the Qinghai-Tibetan Plateau. We collected 422 individuals from 42 natural populations of three major varieties classified under this species. In conifers, mitochondrial (mt) DNA and chloroplast (cp) DNA dispersed by seeds or pollen experience very different levels of gene flow. To this end, we examined the sequence variation of two mtDNA fragments (nad5 intron 1 and nad1 intron b/c) and three cpDNA fragments (trnL-trnF, trnS-trnG and nadhK/C). We found that cpDNA probably introgressed from P. purpurea into remote populations of P. likiangensis through long-distance dispersal. Multiple refugia seem to have been maintained for P. likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions. Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations. However, genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions, which may result from the long-distance dispersal of the cpDNA, as well as its fast lineage sorting during intraspecific divergences. Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers, which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa. Together, the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion, long-distance dispersal, and intraspecific divergences at two sets of DNA genomes with different rates of gene flow.