Species of the genus Bartonella are involved in an increasing variety of human diseases. In addition to the 14 currently recognized species, several Bartonella strains have been recovered from a wide range of wild and domestic mammals in Europe and America. Such a high diversity of geographic distributions, animal reservoirs, arthropod vectors and pathogenic properties makes clarification of our knowledge about the phylogeny of Bartonella species necessary. Phylogenetic data have been inferred mainly from 16S rDNA, 16S--23S rRNA intergenic spacer, citrate synthase and 60 kDa heat-shock protein gene sequences, which are available in GenBank. Comparison of phylogenetic organizations obtained from various genes allowed six statistically significant evolutionary clusters to be identified. Bartonella bacilliformis and Bartonella clarridgeiae appear to be divergent species. Bartonella henselae, Bartonella koehlerae and Bartonella quintana cluster together, as well as Bartonella vinsonii subsp. vinsonii and B. vinsonii subsp. berkhoffii. The fifth group includes bacteria isolated from various rodents that belong to native species from the New World and in the sixth, Bartonella tribocorum, Bartonella elizabethae and Bartonella grahamii are grouped with several strains associated with Old World indigenous rodents. The position of the other species could not be consistently determined. As some cat- or rodent-associated Bartonella appeared to cluster together, it has been suggested that these bacteria and their reservoir hosts may co-evolve. Lack of host specificity, however, seems to be frequent and may reflect the influence of vector specificity. Host or vector specificity may also explain the current geographic distribution of Bartonella species.