Trees produce pollen during specific times of the year. Pollen can induce pollinosis, a type of allergic rhinitis, in humans. In Japan, allergenic pollen is mainly dispersed from February to May. Using data collected at 120 observation sites managed by the Japanese Ministry of the Environment, we studied the annual patterns of airborne allergenic pollen. The allergenic pollen showed an alternating ON-OFF cycle, but the length of the cycle differed among regions. We used an in-phase/out-of-phase analysis to quantify two characteristic features of the synchronisation. The degrees of phase synchronisation were strong in eastern and weak in western Japan. The pattern of allergenic pollen dispersal throughout Japan is typical intermittent synchronisation. This is the first study to evaluate allergenic pollen's distribution from a phase synchronisation viewpoint.