We investigated the social organization of Bonin flying foxes (Pteropus pselaphon) in a roost and the seasonal shift of roosting sites in relation to the reproductive cycle on Chichi-jima Island, Ogasawara (Bonin) Islands, Japan. Using radiotracking, we found that flying foxes formed a colonial roost in a specific area of the island during winter and were more widely dispersed in summer. Although summer roosts were used by solitary flying foxes or nursing females, the winter roost consisted of about 100 individuals. Flying foxes formed ball-shaped, dense clusters in the winter roost. We found 6 roosting groups of clustered bats classified into 3 groups in relation to sex and age: 1) multiple females with a few males, 2) multiple males, and 3) subadults of both sexes. Copulation attempts were not observed in the summer roosts but frequently were observed in type 1 groups in the winter colonial roost. Based on the emergence of newly born pups and the estimated period of pregnancy, fertilization is likely to occur in the winter colonial roost. We conclude that the winter colonial roost plays an important role as a mating site.