Phylogeographic studies revealed that alpine plants, including species distributing in the Arctic, harboured unique genetic structure in central Japan, indicating that alpine plants persisted in the Japanese archipelago throughout Pleistocene climatic oscillations. In contrast, recent long-distance dispersal cannot be discarded for their colonization history, especially for species with adaptation to long-distance seed dispersal such as Vaccinium vitis-idaea (Ericaceae). Here we conducted phylogeographic study based on chloroplast and nuclear markers and examined the biogeographic history of V. vitis-idaea in the Japanese archipelago. Widespread alleles were dominated throughout species’ range in both markers. Although these alleles were also dominated in the Japanese archipelago, unique alleles were exclusively found in some populations in Japan. Recent long-distance dispersal could not explain the exclusive occurrence of unique alleles in the archipelago, suggesting persistent populations of V. vitis-idaea. In addition, the existence of widespread alleles in the Japanese archipelago indicates that secondary colonization also occurred in this region.