To estimate the prevalence of Bartonella in small mammals of different species, during different seasons, and at different study sites, and to provide baseline data for the risk assessment of human Bartonella infection, we captured small mammals using snap traps in Zhejiang Province, China. Bartonella species were detected in small-mammal samples by polymerase chain reaction and positive amplicons were sequenced. Bartonella DNA was detected in 47% (90/192) of Apodemus agrarius, 31% (14/45) of Rattus losea, 16% (7/43) of Rattus norvegicus, 24% (9/37) of Eothenomys melanogaster, 4% (1/28) of Niviventer confucianus, 30% (7/23) of Suncus murinus, 22% (2/9) of Microtus fortis, 27% (2/7) of Rattus tanezumi, and 29% (2/7) of Apodemus peninsulae. No Bartonella DNA was detected in 27 unidentified Soricidae or nine Mus musculus. This is the first report of Bartonella DNA detected in E. melanogaster and N. confucianus. The prevalence of Bartonella DNA varied among small-mammal species, study sites, and seasons; the prevalence of Bartonella DNA between genders did not vary significantly within a species. The sequences we report were most similar to Bartonella grahamii.