We investigated the prevalence of Bartonella infections in ticks, mites and small mammals (rodents, insectivores and weasels) collected during 2001 through 2004, from various military installations and training sites in Korea, using PCR and sequence analysis of 16S rRNA, 23S rRNA and groEL heat shock protein genes. The prevalence of Bartonella spp. was 5.2% (n = 1, 305 sample pools) in ticks, 19.1% (n = 21) in mesostigmatid mites and 13.7% (n = 424 individuals) in small mammals. The prevalence within the family Ixodidae was, 4.4% (n = 1, 173) in Haemaphysalis longicornis (scrub tick), 2.7% (n = 74) in H. flava, 5.0% (n = 20) in Ixodes nipponensis, 11.1% (n = 9) in I. turdus, 33.3% (n = 3) in I. persulcatus and 42.3% (n = 26) in Ixodes spp. ticks. In rodents, the prevalence rate was, 6.7% (n = 373) in Apodemus agrarius (striped field mouse) and 11.1% (n = 9) in Eothenomys regulus (Korean red-backed vole) and in an insectivore, Crocidura lasiura, 12.1% (n = 33). Neither of the two weasels were positive for Bartonella spp. Phylogenetic analysis based on amino acid sequence of a portion of the groEL gene amplified from one A. agrarius spleen was identical to B. elizabethae species. We demonstrated the presence of Bartonella DNA in H. longicornis, H. flava and I. nipponensis ticks, indicating that these ticks should be added to the growing list of potential tick vectors and warrants further detailed investigations to disclose their possible roles in Bartonella infection cycles.