Previous phylogeography on Japanese alpine plants exhibited intra-specific geographic differentiation between populations in central and northern Japan across various taxa. Accordingly, their biogeographic history in the Japanese archipelago was hypothesized that independent coloni- zation into the archipelago occurred at least twice and that populations in central Japan have been persisted with isolation from the northern region. In addition, although northern populations har- boured mostly homogenous genetic structure due to a single expansion history, unique genetic structure was sometimes detected in populations of Tohoku. Such unique genetic structure, but with less consistent tendency, implied that disjunct populations were also persisted in this region. Here, we attempted to examine these biogeographic hypotheses by conducting phylogeographic investigation of Phyllodoce aleutica (Ericaceae). Based on haplotype distribution of chloroplast DNA, populations in central Japan harboured a distinct genetic structure from those in northern Japan. This geographic pattern is consistent with the persistence of isolated populations in central Japan. In addition, populations in Tohoku harboured haplotypes exclusively found in this region, which emphasised the relict populations in this region distinct from other regions. Thus, our study confirmed the north-south differentiation of alpine plants in P. aleutica and suggests the impor- tance of future study focusing on Tohoku region.