Microbial communities are a key element of soil quality and fertility. This research aims to survey the effect of genetically modified cotton cultivar Coker, harbors an endochitinase gene (chi) from Phaseolus vulgaris (bean) on soil bacterial communities. The transgenic chi-resistant cotton (GM), line R8 was selfed for four generations and the corresponding original plant line 1011, wild-type (WT) were provided and planted in the transgenic greenhouse (Biosafety Level 2) at Agricultural Biotechnology Research Institute of Iran (ABRII). Samples of soil were collected from rhizosphere and bulk area of 30, 60 and 90 days old plants. Enumeration of total bacteria and Actinomycetes were carried out using TSA, Water Agar and ISP2 media. Soil DNA was extracted from 1-g samples by using an Ultra Clean soil DNA kit. PCR–DGGE (Denaturing Gradient Gel Electrophoresis) was performed to show diversity in different groups of bacteria. Total numbers of bacteria in soil samples was approximately 106 and 107 CFU/g of dried soil of rhizosphere and bulk soil respectively. Average number of total soil bacteria and Actinomycetes were higher in rhizosphere area of 30 and 60 days old GM plants compared to the control. Although, at the end of growth period (90 days) GM (transgenic) and non-GM plants were approximately equal in number of bacteria around their roots. Molecular analysis based on PCR-DGGE revealed similar microbial dynamics for both Actinomycetes and total batera. The data presented here showed no consistent statistically significant differences in the numbers of total bacteria and Actinomycetes between rhizosphere and bulk soil of chi and non-chi cotton at the end of the experiment. Furthermore, it seems that the growth stage of plant exerts a noticeable effect on the microbial community.