A group of strains isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru were characterized by genotypic, genomic and phenotypic methods. All strains possessed identical 16S rRNA gene sequences that were 99.9 % identical to that of Bradyrhizobium lablabi CCBAU 23086T. Despite having identical 16S rRNA gene sequences, the Phaseolus lunatus strains could be divided into two clades by sequence analysis of recA, atpD, glnII, dnaK and gyrB genes. The genome sequence of a representative of each clade was obtained and compared to the genomes of closely related species of the genus Bradyrhizobium. Average nucleotide identity values below the species circumscription threshold were obtained when comparing the two clades to each other (88.6 %) and with all type strains of the genus Bradyrhizobium(≤92.9 %). Phenotypes distinguishing both clades from all described and closely related species of the genus Bradyrhizobium were found. On the basis of the results obtained, two novel species, Bradyrhizobium paxllaeri sp. nov. (type strain LMTR 21T = DSM 18454T = HAMBI 2911T) and Bradyrhizobium icense sp. nov. (type strain LMTR 13T = HAMBI 3584T = CECT 8509T = CNPSo 2583T), are proposed to accommodate the uncovered clades of Phaseolus lunatus bradyrhizobia. These species share highly related but distinct nifH andnodC symbiosis genes. © 2014 IUMS.