In February 2004, we captured 221 rodents and shrews in the Greater Jakarta area as part of a study to determine the prevalence of rodent-associated vector-borne infections. Microscopic examination of blood smears revealed 6% (13/218) to be positive for Bartonella spp. The corresponding DNA samples, either from blood blots or frozen spleen pieces and from fleas collected on these animals, were tested for evidence of Bartonella infection by PCR, targeting the portions: 378bp and 930bp of the citrate synthase gene (g/tA). The sequences from our sample clusters with a Peruvian entity, B. phoceensis, B. rattimassiliensis and B. elizabethae, the latter species has been associated with endocarditis and neuroretinitis in humans. As previous analyses have shown, there appears to be little geographic or host consistency with phylogenetic placement. The public health significance of these findings remains to be determined.