Knowledge of food habits is essential for understanding the life history of a species; however, such information about the enigmatic Murina genus of bats is little known. In this study, we examined the food habits of Murina hilgendorfi and Murina ussuriensis over four years in Hayakawa, central Japan, using traditional morphological fecal analysis. Both species consumed wingless arthropods (caterpillars and spiders), insects that rarely fly (ground beetles and bush crickets), or diurnal insects (dragonflies and hoverflies), which is a clear indication of gleaning behavior in these bats. In spring, the large-bodied M. hilgendorfi more frequently consumed hard-bodied insects such as beetles and bush crickets, whereas the small-bodied M. ussuriensis more frequently consumed soft-bodied insects such as caterpillars, moths, spiders, and dipterans, suggesting that body size difference influences their food habits, which may have contributed to food resource partitioning between these closely related bats. For M. hilgendorfi, beetles were the main prey in spring and autumn, while caterpillars and grasshoppers were more frequently consumed in spring and autumn, respectively, suggesting that they may have changed prey items according to seasonal fluctuations in food availability.