In December 2005, three bats of indeterminate identity were captured in northern Japan. Their forearm lengths were slightly smaller than the average for Vespertilio sinensis. We identified these three individuals as V. murinus using both morphological and molecular approaches, and discussed their possible migration or vagrancy routes. Prior to the first record of V. murinus on Rebun Island near Hokkaido in 2002, there was no record of this species in Japan. These new occurrences illustrate the importance of determining possible migration or vagrancy routes of bats for understanding and preventing the spread of zoonotic diseases.