(1) Background: Bartonella spp. are Gram-negative, facultative, intracellular bacteria transmitted by hematophagous insects. Several species cause zoonotic diseases such as cat-scratch disease. Bartonella henselae and Bartonella clarridgeiae are the main species found in Thailand, however, there have been few studies on Bartonella spp. In addition, the hematological evaluation of Bartonella-infected animals is limited in Thailand. The aims of this study were prevalence investigation and hematological evaluation of Bartonella-infected dogs and cats residing in Bangkok, Thailand. (2) Methods: In total, 295 dogs and 513 cats were molecularly evaluated to detect Bartonella spp. using PCR with primers targeting the partial gltA, rpoB, ftsZ, ribC, and groEL genes. In total, 651 domestic animals were evaluated for hematological parameters compared between Bartonella-positive and Bartonella-negative animals. (3) Results: Overall, the prevalence of Bartonella spp. was 1.61% which was found only in free-ranging cats (2.83%). Bartonella henselae and B. clarridgeiae were confirmed from a concatenated phylogenetic tree of partial gltA and ribC genes, with 100% bootstrapping replication. For other housekeeping gene sequences, mixed infection was expected from the amplicons of rpoB, ftsZ, and groEL. Importantly, the mean corpuscular volume (MCV) was significantly increased in Bartonella-positive cats. (4) Conclusions: We suggest that B. henselae and B. clarridgeiae are important species and are still circulating in domestic animals, especially cats. The evaluation of blood parameters, especially a raised MCV, should be of concern in Bartonella infection in asymptomatic cats. Additionally, the knowledge of how to prevent Bartonella-related diseases should be promoted with people in at-risk situations.