In our previous study, a genetically-modified (GM) rhizosphere bacterium, Pseudomonas putida strain 101-97 harboring the chitinase-expression vector pKAC9-p07, showed over-production of chitinase and suppressed the damping-off of cucumber seedlings caused by the plant-pathogenic fungus Rhizoctonia solani. To assess the effects of the GM bacterium on other soil microorganisms, we monitored the microbial population in the cucumber rhizosphere after inoculation with the GM bacterium by culture-dependent and -independent methods. In the culture-dependent analysis, total bacterial and fungal populations in the cucumber rhizosphere did not differ after inoculation with either the GM bacterium or its parental strain, P. putida 101R. In the culture-independent analysis, we determined changes in the microbial communities by PCR-denaturing gradient gel electrophoresis (DGGE). The DGGE profiles of bacterial 16S rDNA genes differed significantly depending on whether they had been inoculated with the GM bacterium or its parental strain, whereas the profiles of fungal 18S rDNA genes remained similar.