In alpine ecosystems, the steep environmental gradients produced by the difference in snowmelt timing create a dynamic selective regime for alpine plants. As these gradients directly alter flowering phenology, they can affect pollen-mediated gene flow among populations of single and related species. In northern Japan, we found a hybrid zone dominated by fertile F1s of two alpine shrub species, Phyllodoce caerulea and P. aleutica, along a snowmelt gradient. Seed germination confirmed the fertility of F1 hybrid, making the rarity and absence of backcross and F2 plants puzzling. The long-term clonal perpetuation of F1 hybrids (at least a few thousand years ago) contributes the maintenance of this unique hybrid zone. The distribution patterns of chloroplast DNA haplotypes suggest that F1 formation might be caused by directional pollen flow between parental species along the snowmelt gradient. Based on these results, we discuss the ecological and evolutionary significance of this unique hybrid zone.