Abstract Aim Geographic affinities were analysed for nodule bacteria (Bradyrhizobium sp. Jordan) associated with two legume trees indigenous to the Philippines: Pterocarpus indicus (Papilionoideae) and Wallaceodendron celebicum (Mimosoideae). Location Nodule bacteria from Luzon, the Philippines, were compared with reference strains from Central America, eastern North America, Japan, Korea, China and Australia. Methods Two PCR assays targetting length polymorphisms in the rRNA region were carried out on 96 Philippine bacterial isolates. A 496-bp portion of the 23S rRNA gene was sequenced in 14 representative isolates. Eight strains were analysed in greater depth by sequencing portions of four other genes (16S rRNA [1410 bp], dnaK [603 bp], nifD [822 bp], recA [512 bp]), and phylogenetic trees were constructed by maximum parsimony, neighbour joining and maximum likelihood methods. Results Most of the Philippine Bradyrhizobium strains showed greater similarity to reference strains from Central America than to strains from other source regions included in the analysis. However, phylogenetic trees for the five genes had significantly conflicting topologies, suggesting that lateral gene transfer events had altered genealogical relationships at different loci. In particular, two Philippine strains resembled Bradyrhizobium strains from Central America or China for 16S rRNA, dnaK and recA sequences, but had nifD sequences that clustered with Australian strains (with bootstrap support values of 90–96%). Main conclusions The Philippines have been colonized by Bradyrhizobium strains from multiple source regions. Subsequent lateral gene transfer has resulted in the evolution of Bradyrhizobium strains that combine DNA segments of different geographic origin.