The study of mobile animals such as flying foxes in insular habitats involves clarifying the population status on each island and determining the factors affecting movement patterns among the islands in their distributional range. We visited 25 of the Okinawa Islands and documented the number of Orii's flying foxes Pteropus dasymallus inopinatus from August 2005 to May 2006. We also conducted a monthly road census on the main island (Okinawa-jima Island) and six adjacent islands from June 2006 to January 2007 and counted the number of fruit-bearing trees of the bats' four main food plants. The results of classification and regression tree analysis suggested that distance from the main island was a primary factor in determining the distribution pattern and population size of this flying fox, whereas island area, number of plant species, and food availability did not directly affect population size. The number of flying foxes on each island tended to decrease with an increase in distance from the main island; no flying foxes existed on islands [30 km away from the main island. On the other hand, the results of the monthly census showed that the population size on each island fluctuated seasonally. Individuals may move between islands in response to seasonal changes in food availability. In conclusion, the distribution and abundance of Orii's flying foxes in the Okinawa Islands may be determined by the rate of immigration/emigration, depending on each island's distance from the main island. Seasonal changes in food availability may act as a trigger for interisland movement, but that movement may be restricted by island connectivity.