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<i>Bartonella</i> spp. are Gram-negative zoonotic bacteria transmitted to humans via various blood-sucking arthropods. Rodents have been identified as reservoir hosts of several zoonotic pathogens, including <i>Bartonella</i> spp. In Thailand, studies of <i>Bartonella</i> spp. in rodents from urban areas are limited; thus, a study in this area is necessary. The objectives of this study were to detect <i>Bartonella</i> spp. in rodents in Thailand and to compare the species’ distribution across different areas. In total, 70 blood samples from rodents in urban and suburban areas were tested for <i>Bartonella</i> spp. using a conventional polymerase chain reaction that targeted the citrate synthase (<i>gltA</i>) gene. All <i>Bartonella</i>-positive sequences were analyzed using polymorphism in order to build a phylogenetic tree. Approximately 38% of the rodents studied contained <i>Bartonella</i> DNA. Both <i>Rattus exulans</i> (Pacific rat) and <i>R. tanezumi</i> (Asian house rat) contained <i>Bartonella</i> spp. Four species of <i>Bartonella</i> were detected in blood samples: <i>B. tribocorum</i>, <i>B. phoceensis</i>, <i>B. grahamii</i>, and <i>B. rattimassiliensis</i>. In addition, eight Pacific rats contained the <i>B. kosoyi</i>–<i>B. tribocorum</i> complex. <i>Bartonella phoceensis</i> and <i>B. tribocorum</i>–<i>B. kosoyi</i> complexes were found in a specific habitat (<i>p</i> < 0.05). Interestingly, only seven haplotypes were identified in the sequences analyzed, and only haplotype A was found in both rodent species. Finally, a monitoring program for zoonotic <i>Bartonella</i> infection, especially the <i>B. kosoyi</i>–<i>B. tribocorum</i> complex, <i>B. phoceensis</i>, <i>B. grahamii</i>, and <i>B. rattimassiliensis</i> should be established, especially in high-risk areas.