Flying squirrels have important roles in ecosystems, dispersing seeds and spores. However, flying squirrel species, which strongly depend on old mature forests, have declined in abundance due to the logging of mature forests. Guidelines for the conservation of flying squirrels have been developed, but it is vital to have an accurate understanding of their ecology to revise the guidelines to be more effective. The Japanese flying squirrel (Pteromys momonga, JFS), endangered in wide areas of Japan, is one of the flying squirrel species for which the least ecological information is available. This paper reviews individual reports and attempts to address knowledge gaps in JFS ecology to facilitate conservation strategies. Of particular importance is the fact that JFS uses planted Japanese cedar (Cryptomeria japonica) for nesting, gliding and winter forage, and JFS habitat may be strongly influenced by human activities such as forestry. Plantations are regularly logged, so management of plantations needs to be implemented with attention to the JFS habitat. It was also found that some ecological information necessary to develop guidelines for conservation, such as diet, gliding ability, and home-range size, is missing. Clarification of these issues is an important task.