Assays with seven sets of lineage-specific polymerase chain reaction (PCR) primers in the ribosomal RNA region were performed on 96 isolates of the Bradyrhizobium sp. nodule bacteria from Barro Colorado Island, Panama. The isolates were derived from 10 legume host species in six genera (Centrosema, Desmodium, Dioclea, Inga, Machaerium and Vigna). The PCR assays differentiated 13 composite genotypes, and sequencing of a 5′ 23S rRNA region indicated that all but one had a unique sequence. The most common genotype (seen in 44% of the isolates) was associated with all six legume host genera, and had a marker profile and 5′ 23S rRNA sequence identical to a Bradyrhizobium lineage associated with several other legume genera in Panama and Costa Rica. Another 46% of the isolates had genotypes found to be associated with two to three legume genera. Bradyrhizobium strains with low host specificity thus appear to be prevalent in this tropical forest. Based on 16S rRNA and 5′ 23S rRNA markers, most of the isolates had clear affinities to either B. japonicum or B. elkanii. However, one strain (Cp5–3) with a B. elkanii-type 16S rRNA marker had a 5′ 23S rRNA region resembling B. japonicum. A partition homogeneity test indicated that relationships of strain Cp5–3 were significantly discordant for 16S rRNA vs. 23S rRNA sequences, and a runs test detected significant mosaic structure across the rRNA region. Lateral gene transfer events have therefore played a role in the evolution of symbiotic bacteria in this environment.