Airborne microorganisms transported from forested areas can influence cloud formation by forming ice nuclei. However, the vertical transportation of airborne microorganisms over forested areas is not well understood. We collected aerosols at three heights, [ground (2 m), canopy top (20 m), and above canopy (500 m)] during the summer, fall and winter, to analyze the airborne microbial communities that were distributed vertically over the forest. During summer and fall, the microbial particles maintained similar concentrations in the forest zone (canopy top and ground) and decreased to 1/10th of the microbial concentration in the above canopy area. The particle concentrations in winter indicated efficient vertical mixing below 500 m. High-throughput DNA sequencing revealed that the airborne microbial communities were composed of terrestrial and phyllospheric species associated with the degradation of decaying plant litters. Regardless of the three seasons, the above canopy was dominated by atmospheric stress-resistant bacteria from the phyla Actinobacteria and Firmicutes. Unlike bacteria, the mushroom-type fungal members of Agaricomycetes grew in relative abundance above the canopy, primarily throughout the summer and winter, while mold-type fungal Dothideomycetes species were often found at all three heights during the fall. The Fusarium, Pseudomonas, and Bacillus isolates, which were obtained from air samples at three heights, indicated high activities of ice nucleation in the water-drop freezing assay. Therefore, ice-nucleating microbial taxa likely originated from fungal and bacterial communities in the soil litter and plant surfaces of the phyllospheric environments.