Bacterial strains are a characteristic feature of many bacterial pathogens, including the species of the genus Bartonella. These bacteria are associated with different vertebrate hosts and vectors and have been detected in North America, Australia, Asia, and Europe. This study presents molecular characterization of Bartonella strains circulating in wild rodents. B. taylorii and B. grahamii are detected with high prevalence in mice, voles, and rats. However, there is a lack of knowledge on the geographical distribution and genetic diversity of B. taylorii and B. grahamii strains in wild rodents. The objectives of this study were to characterize the genetic diversity of B. taylorii and B. grahamii strains by sequence analysis of the housekeeping gene (rpoB) and the 16S-23S rRNA intergenic species region (ITS). Sequence analysis of rpoB gene revealed the presence of 15 B. taylorii genotypes and four B. grahamii genotypes in mice and voles captured in Lithuania. Sequence analysis of the ITS region revealed the presence of six B. taylorii genotypes and four B. grahamii genotypes in Lithuanian voles and mice. Analysis of genetic diversity demonstrated that B. grahamii strains derived from the same geographic region or from regions of close proximity more conservative, while B. grahamii strains from more distant areas are more variable. Genetic diversity of B. taylorii strains seems not to depend on geographic distance.