To improve our understanding of evolutionary forces acting on Legionella species, we performed comparative genomic analyses to elucidate population structure and estimate the effects of homologous recombination. The analysis set consisted of 10 published and 33 Legionella genomes sequenced in this study, including Legionella species occasionally reported as etiologic agents of human disease and Lp subtypes 2 through 17 (Table 1). Genomes were assembled using a hybrid assembly of Roche 454 and Illumina in this study where each genome project contained at least 3 million sequencing reads (combined Illumina and 454 sequencing technologies) (Supplementary Table 1).