[Objective] Bartonella quintana, transmitted by the body louse (Pediculus humanis), is the etiologic agent of a variety of disease manifestations in humans including trench fever. To further confirm if macaques can be the natural reservoir of B. quintana, we studied the infections of B. quintana in the experimental macaque populations from the four regions in China and characterized the islolates of B. quintana originated from the macaques.[Methods] The samples of blood and serum collected from 550 macaques were used to isolate strains, detect the specific nucleic acid fragment and test IgG antibody. The molecular taxonomic characterization and nucleotide polymorphisms of the strains were analyzed based on the sequences of the six housekeeping genes using PCR, sequecing and phylogenetic analysis. The fingerprint pattern of random amplified polymorphic DNA (RAPD) were also used to discriminated the stains from the different hosts by the three random primers. The IgG antibody anti-B. quintana were detected using indirect iocmmunofluorescence assay (IFA).[Results] Totally, 8 strains of B. quintana were isolated from 5 females and 3 males from 250 rhesus macaques in Sichuan province, with 3.2% infection rate. Our molecular test, detecting 550 blood samples using qPCR with a total of 8.2% infection rate of B. quintana, showed that the prevalence of macaques from Sichuan was significantly higher than that of the macaques from the other areas. The seropositivity rate was 19.0% in the rhesus macaques which was higher than that of the cynomolgus macaques (5.6%) and there was no difference between males and females and among the different areas. The RAPD-figerprints of the strains from the rhesus macaques in Sichuan province have an identical 8-bands pattern and was discriminated from the pattern of B. henselae. While the fingerprint of the human str. Fuller of B. quintana showed a 6-bands pattern. According to the nucleotide polymorphism analysis, the strains of B. quintana from different hosts show obvious genetic diversity. There was a higher diversity between the monkey strains and the human strains and a smaller difference among the monkey strains.[Conclusion] There are high prevalence of B. quintana in the macaques population in China. The natural infection rate and antibody level in the rhesus macaques were significantly higher than that of the cynomolgus macaques. The genotype of the strains originated from the macaques is different from that of the strains from human. We demonstrated that the macaques are the natural reservoir of B. quintana.