The Bartonella species are zoonotic agents that infect mammals and are transmitted by arthropod vectors. Approximately 18 distinct genotypes cause diseases in humans, and may be spread by both domestic and wild animals. In Brazil, Bartonella genotypes have been identified in several species of wild mammals, and in the present study, we analyzed samples from non-human primates (marmosets), marsupials, rodents, and bats, and compared them with the genotypes described in mammals from Brazil, to examine the distribution of Bartonella genotypes in two impacted areas of Rio de Janeiro state, in southeastern Brazil. We used polymerase chain reaction (PCR) methods to detect the Bartonella DNA using partial sequences of the gltA, ftsZ, and groEL genes. We generated Bayesian inference and maximum likelihood trees to characterize the positive PCR samples and infer the phylogenetic relationships of the genotypes. A total of 276 animals were captured, including 110 bats, 91 rodents, 38 marsupials, and 37 marmosets. The DNA of Bartonella was amplified from tissue samples collected from 12 (4.34%) of the animals, including eight rodents – Akodon cursor (5/44) and Nectomys squamipes (3/27) – and four bats, Artibeus lituratus (3/58) and Carollia perspicillata (1/15). We identified Bartonella genotypes closely related to those described in previous studies, as well as new genotypes in both the rodent and the bat samples. Considering the high diversity of the Bartonella genotypes and hosts identified in the present study, further research is needed to better understand the relationships between the different Bartonella genotypes and their vectors and host species. The presence of Bartonella in the wild rodents and bats from the study area indicates that the local human populations may be at risk of infection by Bartonella due to the spillover of these strains from the wild environment to domestic and peri-domestic environments.