We conducted a multilocus enzyme electrophoresis (MLEE) study to assess the genetic structure of the nitrogen-fixing bacteria Rhizobium etli bv. phaseoli. We analysed the genetic variation at 10 enzyme-encoding chromosomal loci of 482 isolates from root nodules of Phaseolus vulgaris and P. coccineus bean plants. The isolates were obtained from six traditionally managed agricultural plots in two localities in the State of Puebla, in Central Mexico. The total mean genetic diversity (HE) for the six plots was 0.531. Among the 482 isolates collected, 126 distinctive multilocus genotypes (electrophoretic types [Ets]) were obtained, and approximately half of the isolates are represented by five widespread ETs. A significant degree of genetic differentiation among the six plots (GST = 0.072) and between the two localities (GST = 0.022) was detected. The main part of the observed variability (70%) was found among the isolates within the plants. The cluster analysis revealed two deeply diverging lineages, separated at a genetic distance of 0.7. When a multilocus linkage disequilibrium analysis was performed at different hierarchical levels, we found significant linkage disequilibrium, but when the analysis was performed for the genotypes within the two diverging lineages, we found evidence of recombination. We propose for R. etli bv. phaseoli a reticulated and epidemic genetic structure, in which few genotypes increase in frequency to produce numerically dominant clones, and genetic exchange occurs mainly among genotypes within each lineage.