The release of genetically modified (GM) crops has potential to alter the bacterial population within rhizosphere. Here, the potential effect of GM maize cv. IE09S034 containing the Cry1Ie toxin gene from Bacillus thuringiensis (Bt) was investigated under the field conditions. The community composition and the relative abundance of the bacteria in rhizosphere soil were estimated by analysing 16S rRNA PCR amplicons. Our results indicated that Bt maize IE09S034 has no significant effects on the rhizosphere bacterial community. Instead, it was found that factors such as plant growth stage and year have a stronger effect on the bacterial population dynamics. Our findings therefore provide reliable evidence supporting the potential commercial cultivation of the cv. IE09S034.