In consideration for the increasing widespread use of genetically modified (GM) crops, one of the important issues for assessment is the effect of GM crops on soil microbial communities.In this study, T chitinase-transgenic cotton (line #57) and its non-transgenic line were investigated for bacterial and fungal dynamics during its development stages.The assessments were performed by viable plate count and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assays.Viable plate count analysis showed an increase in community structures and the number of culturable bacteria in rhizosphere of both transgenic and non-transgenic cultivars as compared to bulk soil. PCR-DGGE confirmed results of viable plate count assays of the changes in bacterial and fungal communities for all cotton development stages in rhizosphere and bulk zones. No significant differences in number of functional bacteria were observed between rhizosphere soil of chitinase transgenic and non-chitinase transgenic cotton at one particular stage.The results indicated that T chitinase-transgenic cotton (line #57) might have no adverse effects on community structures and total number of culturable bacteria and fungi in the rhizosphere.