Hybrid zones between species with staggered reproductive phenology sometimes occur along elevational gradients. The maintenance of such hybrid zones may depend on elevational shift in phenology and vertical dispersal of pollen and seeds. In a hybrid zone of Cerasus leveilleana (Cl) and C. sargentii (Cs), 111 adults, 372 embryos of 65 mothers, and 133 juveniles were sampled across elevations of 900–1,400 m in central Japan. Using the hybrid index estimated from nuclear microsatellites, the samples were assigned to Cl, Cs or their hybrid taxon. Cs was in higher elevations than Cl with an overlapping range, and their hybrids were in intermediary elevations. Flowering periods were earlier in Cs than in Cl with little overlap at the same elevation and were intermediate in their hybrids. Flowering periods were delayed in higher elevations and overlapped between Cl and Cs in different elevations. Fruiting periods were slightly earlier in Cs than in Cl but were largely overlapped. Effective pollinators and seed dispersers were common among the taxa. Changes in the hybrid index from mothers to their embryos were larger in hybrid mothers than in Cl or Cs mothers, indicating mating of hybrids with diverse taxa. In Cs, juveniles were more abundant in lower elevations than embryos, indicating downhill seed dispersal. Proportions of hybrids were 19% in embryos, 17% in juveniles and 12% in adults. The findings suggest that the hybrid zone is maintained by interspecific pollination between different elevations, backcrossing with hybrids at similar elevations, vertical seed dispersal and mild selection against hybrids.