Investigations of the population genetics of Bartonella henselae have demonstrated a high level of diversity among strains, and the delineation of isolates into one of two subtypes, type I (Houston) and type II (Marseille), represented by specific 16S ribosomal DNA (rDNA) sequences, has long been considered the most significant genotypic division within the species. This belief is challenged by recent work suggesting a role for horizontal gene exchange in generating intraspecies diversity. We attempted to resolve this issue and extend exploration of the population structure of B. henselae by using multilocus sequence typing (MLST) to examine the distribution of polymorphisms within nine different genes in a sample of 37 human and feline isolates. MLST distinguished seven sequence types (STs) that resolved into three distinct lineages, suggesting a clonal population structure for the species, and support for these divisions was obtained by macrorestriction analysis using pulsed-field gel electrophoresis. The distribution of STs among isolates recovered from human infections was not random, and such isolates were significantly more often associated with one particular ST, lending further support to the suggestion that specific genotypes contribute disproportionately to the disease burden in humans. All but one isolate lay on lineages that bore the representative strain of either the Houston or Marseille subtype. However, the distribution of the two 16S rDNA alleles among the isolates was not entirely congruent with their lineage allocations, indicating that this is not a sensitive marker of the clonal divisions within the species. The inheritances of several of the genes studied could not be reconciled with one another, providing further evidence of horizontal gene transfer among B. henselae strains and suggesting that recombination has a role in shaping the genetic character of bartonellae.Bartonella henselae is now well established as a significant human pathogen and is possibly the agent of the world's most common bacterial zoonosis acquired from a companion animal. The bacterium is naturally maintained through persistent, subclinical infections in felids and is transmitted between reservoir hosts via arthropods (Ctenocephalides felis). The prevalence of B. henselae bacteremia in domestic cats ranges from about 10 to 40% (7, 17), and infections have been encountered virtually worldwide. Cat scratch disease (CSD) is the most commonly encountered B. henselae-induced syndrome in humans, with an estimated 25,000 cases and several thousand hospitalizations occurring each year in the United States alone (16,19,21,34). B. henselae is also unique in its invasion mechanism (9) and capacity to drive angiogenesis in vitro and in vivo (20). Although the prevalence of reported CSD and other B. henselae infections is relatively high (10 cases per 100,000 population per annum in the United States), the frequency of human inoculation by B. henselae is likely to be considerably greater, given the high carriage rates in domestic...