Haemophilus ducreyi, the etiologic agent of chancroid, expresses variants of several key virulence factors. While previous reports suggested that H. ducreyi strains formed two clonal populations, the differences between, and diversity within, these populations were unclear. To assess their variability, we examined sequence diversity at 11 H. ducreyi loci, including virulence and housekeeping genes, augmenting published data sets with PCR-amplified genes to acquire data for at least 10 strains at each locus. While sequences from all 11 loci place strains into two distinct groups, there was very little variation within each group. The difference between alleles of the two groups was variable and large at 3 loci encoding surface-exposed proteins (0.4 < K S < 1.3, where K S is divergence at synonymous sites) but consistently small at genes encoding cytoplasmic or periplasmic proteins (K S < 0.09). The data suggest that the two classes have recently diverged, that recombination has introduced variant alleles into at least 3 distinct loci, and that these alleles have been confined to one of the two classes. In addition, recombination is evident among alleles within, but not between, classes. Rather than clones of the same species, these properties indicate that the two classes may form distinct species.Haemophilus ducreyi is a Gram-negative coccobacillus in the family Pasteurellaceae (2) and the causative agent of chancroid, a sexually transmitted, genital ulcer disease which facilitates transmission of 14,23,44). While H. ducreyi was placed in the polyphyletic genus Haemophilus due to its requirement for hemin, Haemophilus species do not form a cohesive group within the Pasteurellaceae (6, 20). The species that are most closely related to H. ducreyi include Actinobacter pleuropneumoniae and Nicoletella semolina (see Fig. S1 in the supplemental material) (16).Previous attempts to examine the diversity within the species H. ducreyi using immunotyping (36) and outer membrane profiling (32) showed very few differences among strains. Molecular analyses showed some differences, e.g., ribotyping of strains from two outbreaks yielded multiple restriction fragment length polymorphism (RFLP) patterns (19), but designations based on these differences have not been widely adopted or used for epidemiologic studies, in part due to the difficulty in culturing this fastidious organism. The lack of a standard typing system makes epidemiologic studies more difficult, and epidemiologic data for chancroid are therefore limited.One way to study diversity in H. ducreyi is to assess its population structure. Whereas the lack of recombination in some bacterial species generates stable clones (5), others recombine sufficiently rapidly to obscure clonal relationships (10, 11). While many Haemophilus species are naturally competent, H. ducreyi is considered nontransformable due to defects in the DNA uptake apparatus (16,34). This would likely decrease rates of recombination and generate stable clones. Initial studies of the clonal structure of...