Haemophilus somnus can be either a commensal of bovine mucosal surfaces or an opportunistic pathogen. Pathogenic strains of H. somnus are a significant cause of systemic disease in cattle. We report the genome sequence of H. somnus 129Pt, a nonpathogenic commensal preputial isolate, and the results of a genome-wide comparative analysis of H. somnus 129Pt, Haemophilus influenzae Rd, and Haemophilus ducreyi 35000HP. We found unique genes in H. somnus 129Pt involved in lipooligosaccharide biosynthesis, carbohydrate uptake and metabolism, cation transport, amino acid metabolism, ubiquinone and menaquinone biosynthesis, cell surface adhesion, biosynthesis of cofactors, energy metabolism, and electron transport. There were also many genes in common among the three organisms. Our comparative analyses of H. somnus 129Pt, H. influenzae Rd, and H. ducreyi 35000HP revealed similarities and differences in the numbers and compositions of genes involved in metabolism, host colonization, and persistence. These results lay a foundation for research on the host specificities and niche preferences of these organisms. Future comparisons between H. somnus 129Pt and virulent strains will aid in the development of protective strategies and vaccines to protect cattle against H. somnus disease.Haemophilus somnus (Histophilus somni), a member of the family Pasteurellaceae (47), can be either a commensal of bovine mucosal surfaces or an opportunistic pathogen. Commensal H. somnus strains colonize and reside relatively harmlessly in the upper respiratory and reproductive tracts, while pathogenic strains spread systemically and cause diseases such as pneumonia, thrombotic meningoencephalitis, myocarditis, septicemia, arthritis, and abortion (10,34,41,42). Here, we report the genome sequence of H. somnus 129Pt, a commensal preputial isolate. We compared H. somnus 129Pt with the finished genomes of Haemophilus influenzae Rd, an avirulent laboratory strain that can invade certain human epithelial cell lines in culture (12), and Haemophilus ducreyi 35000HP, which causes the human sexually transmitted disease chancroid. H. somnus 129Pt and H. influenzae Rd are moderately related (14, 25), do not cause disease, and colonize mucosal niches in different hosts. Phylogenetic analyses have shown that H. ducreyi is not closely related to members of the genus Haemophilus (1, 14, 30) but is a member of the Pasteurellaceae that colonizes genital mucosal surfaces. Its surface lipooligosaccharides (LOS) are similar in structure to those from Haemophilus and Neisseria strains (8), and it occupies a (mucosal) niche similar to that of H. somnus but in a different host. Therefore, the identification of common genes that these organisms share as well as genes unique to each organism may provide some clues about their host specificities and niche preferences.Through a genome-wide comparative analysis of H. somnus 129Pt, H. influenzae Rd, and H. ducreyi 35000HP, we found similarities and differences among these organisms in terms of the numbers and compositions o...