In this study, we uncovered the patterns of DNA shuffling between Legionella species. We showed that, in the core genome, linkage disequilibrium breaks down with increasing genetic distance between markers and that each strain contained regions of its genome most likely to be affected by homologous recombination. Evidence for recombination within the Lp species has been noted previously171845. As expected, the BAPs population structure analysis predicted admixture within Lp populations (Fig. 5). However, our analyses suggest that homologous recombination is almost exclusively an intraspecies event. We could not trace any sources of the potentially recombinant regions identified by ClonalFrame to a source outside of Lp. Population structure analysis in general offered little evidence of interspecies DNA admixture with the odd exception of the L. bozemanii serogroup 2 strain (Fig. 6). Although most accessory genes showed little evidence of interspecies transfer, a significant minority (144/2379) had a phylogenetic pattern consistent with HGT between Legionella spp. We also found near identical versions of two Lp plasmids in other Legionella clades. This pattern of gene flow, mostly occurring within species but with rare instances of sharing between congeners, has been termed ‘fuzzy species’59.