Commercially available DNA microarrays containing genome-wide spotted oligonucleotides encompass the soil bacteria Bacillus subtilis or Streptomyces coelicolor genomes. These have been used to analyse potential differences in rhizobacterial communities of transgenic maize engineered to express the Bacillus thuringensis Cry toxin (Bt maize) in three different agricultural soils. No differences in hybridisation were observed between genetically and non-genetically modified maize rhizobacteria from two Bt lines with a detection sensitivity of five copies of a particular gene above the background. Soil-specific hybridisation results were obtained when rhizobacterial DNA was compared to the corresponding genomic DNA spotted in the microarrays suggesting that the use of genome-wide DNA arrays could serve as a useful tool for the molecular monitoring of rhizobacterial communities.