The magnitude of intraspecific variation in the frequency of multiple paternity, and patterns in its relationship with other variables, was investigated in wild populations of the Japanese wood mouse Apodemus speciosus. The genotypes of 34 females and their offspring were determined on the basis of five microsatellite loci. A high proportion of litters (61.8% = 21/34 litters) were found to have been sired by multiple males. There was high variation in the proportion of multiple paternity in association with sampling localities and/or sampling years (27.3%–78.3%), which was higher than the interspecific variation shown by the proportion of multiple paternity across all studies (40.0%–65.2%) in the genus Apodemus (five species). This large magnitude of intraspecific variation might potentially affect the interpretation in previous studies making interspecific comparisons, and should therefore be taken into account as an important variable.