In Japan, Japanese cedar pollen dispersal is one of the major causes of pollinosis. Sydowia japonica is an ascomycetous fungus that grows exclusively on the male strobili of Japanese cedar, suggesting a possible mechanism for controlling pollen dispersal. To evaluate this possibility, eleven isolates of S. japonica were collected from around Japan and used as an inoculum to male strobili of Japanese cedar. The treatment demonstrated that the fungus infected only the pollen and prevented pollen dispersal. The fungus did not cause any additional symptoms to other parts of Japanese cedar, such as needles, stems, and buds. All S. japonica isolates collected around Japan could serve to control pollen dispersal. Periodic observation of the fungal pathogenesis with stereomicroscope and scanning electron microscope showed that hyphal fragments and conidia of S. japonica germinated on the surface of male strobili, and the germ tube entered pollen sacs through opening microsporophylls. Within the pollen sacs, the hyphae penetrated pollen gradually, such that all pollen was infected by the fungus by approximately one month before the pollen dispersal season. The infected pollen was destroyed due to the fungal infection and was never released. Our data suggests a novel approach of preventing pollen dispersal using pollen-specific fungal infection.