To analyse determinants of biogeographic structure in members of the genus Bradyrhizobium, isolates were obtained from 41 legume genera, originating from North American sites spanning 48.5 6 of latitude (Alaska to Panama). Sequencing of portions of six gene loci (3674 bp) in 203 isolates showed that there was only a weak trend towards higher nucleotide diversity in tropical regions. Phylogenetic relationships for nifD, in the symbiosis island region of the Bradyrhizobium chromosome, conflicted substantially with a tree inferred for five housekeeping gene loci. For both nifD and housekeeping gene trees, bacteria from each region were significantly more similar, on average, than would be expected if the source location was permuted at random on the tree. Within-region permutation tests also showed that bacteria clustered significantly on particular host plant clades at all levels in the phylogeny of legumes (from genus up to subfamily). Nevertheless, some bacterial groups were dispersed across multiple regions and were associated with diverse legume host lineages. These results indicate that migration, horizontal gene transfer and host interactions have all influenced the geographical divergence of Bradyrhizobium populations on a continental scale.