Field trials with the genetic modified (GM) maize stacked hybrid NK603 × MON810 performed in two different locations in the Czech Republic were used for evaluation of genetic diversity of rhizosphere bacterial communities using the terminal restriction fragment length polymorphism. Statistically significant differences in the number of terminal restriction fragments (i.e. bacterial richness) between GM and non-GM maize were not detected. Diversity indices (Gini-Simpson and Shannon’s) revealed higher bacterial diversity in non-GM sample from location Ivanovice na Hané and in the GM maize from location Probluz, but statistical significant differences between GM and non-GM samples were not detected. Additionally, using principal component analysis and cluster analysis, no substantial variation in the composition of bacterial communities between GM and conventional maize were observed but the differences among individual collection sites were recorded.