Abstract: Objective To understand the Bartonella infection status in small rodents in households in western area of Yunnan province. Methods A total of 800 households were randomly selected from 40 natural villages of 10 counties in western Yunnan. Small rodents were captured for 3 consecutive nights in each household. The liver and spleen specimen of small rodents were collected for DNA extraction. The gltA gene of Bartonella was amplified with PCR and gene-sequencing test was conducted for PCR amplification products. Results A total of 421 small rodents, belonging to 9 species, were captured, and 404 specimens were collected and tested with PCR. The Bartonella positive rate was 15.84% (64/404). Of 9 species, the part of specimens from Rattus tanezumi and Rattus norvegicus were positive for Bartonella and the positive rate was 23.05% (62/269) and 8.70% (2/23), respectively. Among 10 counties, the specimens collected from 6 counties were positive. Gene analysis showed that there were 6 gene types of Bartonella infection, which included B. tribocorum, B. queenslandensis, B. elizabethae and B. rochalimae, and 2 possible new gene types were found. Conclusion Bartonella infection was detected in small rodents in households in western Yunnan and the gene diversity was observed. Bartonella infection rate in some counties was high, indicating that the surveillance and control/prevention measures need to be strengthened.