The objective of this work was to evaluate the effect of genetically modified common bean for Bean Golden Mosaic Virus, BGMV, resistance (Olathe M1-4) on nontarget organisms. In a field experiment established in a completely randomized design with two treatments (Olathe Pinto cultivar and M1-4 Olathe elite event), two sampling periods (V4 and R6 stages) and ten replicates, cultivated and non-cultivated bacterial cells from rhizosphere soil and bulk soil were obtained, and their total DNA was extracted. The V6-V8 region of 16S rDNA was amplified for the whole bacterial community, and primers specific for the alpha (&amp;#945;) subgroup of the Proteobacteria phylum were obtained from uncultured cells and used for amplification. Using the Jaccard coefficient and UPGMA (Unweighted pair-group method with arithmetic mean), dendrograms comparing the conventional Olathe Pinto and the elite event Olathe M1-4 transgenic varieties were obtained. The clusters obtained from the 16S rDNA PCR-DGGE profiles indicate changes in the rhizosphere bacterial community in genetically modified plants, being more notable in the profiles obtained for alphaproteobacteria. Sample origin and plant development stages affect bacterial community profiles.