A 168-day microcosms experiment was used to assess the possible functional and structural shifts occurring in the bacterial community of a site with a historical record of polychlorinated biphenyl (PCB) contamination, after the introduction of plants whose roots have been inoculated with genetically modified (GM) microorganisms, designed for rhizoremediation. Salix sp. plants were inoculated with two different GM Pseudomonas fluorescens strains or with their parental wild-type strain. Both bulk soil and rhizosphere samples were analyzed. Physiological profiles based on 31 ecologically relevant carbon sources were used to detect differences in bacterial community functions. The community structure of eubacteria, α and β-proteobacteria, actinobacteria and acidobacteria communities were analyzed via a polymerase chain reaction–thermal gradient gel electrophoresis (TGGE) approach. The introduced transgenes had no effect on the function and structure of the bacterial community in bulk soil, although they enhanced biodegradation of PCBs as determined by chemical analysis. However, the transgenes effected the development of functionally and genetically distinct bacterial communities in the rhizosphere. Moreover, structural and functional differences were detected between planted and unplanted soils and between soil and rhizosphere samples. In the case of the different group-specific structures studied, differences were observed between groups because of time-dependant shifts, rhizosphere effect and bacterial strain introduced.