Ecologic and bacteriologic observations of small mammals captured in Yunnan Province in the People's Republic of China indicated that Bartonella infections occurred at a high prevalence among some rodent species. Sequence analyses of the citrate synthase genes of these Bartonella demonstrated that rodents in this region harbored a diverse assemblage of strains. The Bartonella isolates obtained from Apodemus, Eothenomys, and Rattus typically clustered separately by genus of rodent host. Cultures obtained from Rattus rats were genetically related to Bartonella elizabethae, a recognized human pathogen. The finding of Bartonella species in a high proportion of the rodent samples from Yunnan suggests the need to investigate whether these agents might be responsible for cases of febrile illnesses of unknown etiology in southern China and elsewhere in southeastern Asia.