To maintain local populations of the Siberian flying squirrel Pteromys volans in restricted small habitats, it is necessary to understand their nesting and food biology. Communal nesting of P. volans is well documented in the Eurasian continent, but the details of this behavior have been poorly investigated in Japan. We investigated a group composition of P. volans in Hokkaido, Japan. The mean numbers of individuals using each nest box and tree cavity were 2.17 and 2.44, respectively. Although each female had its own exclusive home range, communal nesting composed by two females was observed in nest boxes. This result suggested that females frequently used nest boxes and formed same-sex groups in urban areas where nest resources might be scarce. Communal nesting of P. volans was found in both nest boxes and cavities with seasonal difference, and cavities were mainly used in winter. Communal nesting of P. volans in Japan may be associated with reproduction, because most cases of communal nesting were composed of one male and one female. To conserve local population of the Siberian flying squirrel, the preservation of cavities, which are usable for more than two individuals, is needed to enable them to breed stably and overwinter safely.