To determine the prevalence of Bartonella species and identify which species of Bartonella naturally infects the striped field mouse (Apodemus agrarius) in the Republic of Korea (ROK), spleens from 200 mice were assayed by nested polymerase chain reaction (nPCR) targeting the RNA polymerase subunit beta (rpoB) gene and the 16S-23S internal transcribed spacer (ITS) region for members of the genus Bartonella. Utilizing PCR techniques, the prevalence of Bartonella spp. ranged from 31.5% (63/200) to 62.0% (124/200) for the rpoB and ITS gene fragments, respectively. The most prevalent species, Bartonella grahamii, was assigned to 17 genotypes and closely related to the zoonotic pathogens, B. taylorii, B. tribocorum, B. phoceensis and B. henselae, which also were detected. Two Bartonella isolates (KRBG28 and KRBG32) were recovered from blood of A. agrarius captured in Gyeonggi Province, ROK. Comparison of the 16S rRNA, hemin-binding protein E (hbpE), glutamate dehydrogenase 1 (gdh1), invasion-associated protein B (ialB), cell division protein (ftsZ), citrate synthase (gltA), 60 kDa heat shock protein (groEL), rpoB gene fragments and the ITS region sequences from the isolates with GenBank was confirmed as B. grahamii. Phylogenetic analysis based on the alignment of concatenated sequences (4933 bp) of KRBG28 and KRBG32 clustered with B. grahamii, forming an independent clade between Asian and American/European B. grahamii genogroups.