Peasants of the Quechua region of the Peruvian Andes use chacras to grow maize (Zea mays) in innate association with bur clover (Medicago hispida). From a total of 25 bacterial strains isolated from root nodules of bur clover grown in soils from chacras in Allpas (Acobamba, Peru) 7 clustered into 6 Repetitive extragenic palindromic-polymerase chain reactions (REP-PCR) groups. The nearly complete 16S rRNA gene sequence from the representative strains AP1, AP15, AP28, AP29, AP37, and AP70 showed they were closely related to members of the genus Ensifer of the Alphaproteobacteria. Sequencing of the housekeeping atpD, glnII, and recA and the symbiotic nodC genes from each of the six strains revealed they all were similar to those of strains included in Ensifer medicae. The remaining 18 strains were distributed into 8 REP-PCR groups and analyses of the 16S rRNA gene sequences showed that the isolates belong to several phylogenetic groups, being closely related to species of genera Kaistia, Pseudomonas, Achromobacter, Stenotrophomonas, Xanthomonas, Sphyngopyxis, Duganella, and Rheinheimera. © 2013 Springer-Verlag Berlin Heidelberg.