A comparison was made of the effect of glyphosate (Roundup®Plus), a post-emergency applied herbicide, and of Harness®GTZ, a pre-emergency applied herbicide, on the rhizobacterial communities of genetically modified NK603 glyphosate-tolerant maize. The potential effect was monitored by direct amplification, cloning and sequencing of soil DNA encoding 16S rRNA, rhizobacterial DNA hybridization to commercially available genome-wide microarrays from the soil bacterium Streptomyces coelicolor, and high-throughput DNA pyrosequencing of the bacterial DNA coding for 16S rRNA hypervariable V6 region. The results obtained strongly suggest that both herbicides do in fact affect the maize rhizobacterial communities, glyphosate being, to a great extent, the environmentally less aggressive herbicide.