A total of 1,835 Yersinia spp. were isolated from 925 (60.5%) of 1,530 wild mice and from 139 (79.9%) of 174 moles living in mountainous areas of eastern Shimane Prefecture, Japan. The Yersinia spp. included 1,106 Yersinia enterocolitica, 26 Y. enterocolitica-like, 176 Yersinia mollaretii, 149 Yersinia frederiksenii, 70 Yersinia intermedia, 231 Yersinia kristensenii, 5 Yersinia aldovae, and 72 Yersinia pseudotuberculosis. Human pathogenic Y. enterocolitica was not isolated. Y. pseudotuberculosis was divided into 10 virulent 40-to 50-MDa plasmid-positive (P+) strains (serotypes lb, 4b, and untypeable) and 62 plasmid-negative (P-) strains (serotypes lb, 2b, 2c, 4a, 5a, 5b, 6, 7, and untypeable). P+ strains of serotypes lb (two strains), 4b (seven strains), and untypeable (one strain) were isolated from nine Apodemus speciosus and one Apodemus argenteus. The isolates of Yersinia spp. were more frequently detected in newborn mice and during the breeding season. The P+ Y. pseudotuberculosis strains were recovered at less than 104 cells per g of the cecal contents. Thus, the prevalence of Yersinia spp. in small wild animals depends on the newborn animals born during the cold months, and wild mice in mountainous areas are important reservoirs of Y. pseudotuberculosis.