Impact of genetically modified or transgenic plants on the eco-environment has aroused great concerns.But little is known of their possible impacts on non-target organisms,such as microbial communities associated with their parent plants in the soil environment because of the complex structure-function relationships of microorganisms.A one-year field study was carried out by analyzing soil samples collected from the cotton field and the rhizospheres of cotton plants of transgenic cotton variety GK12 (expressing Bacillius thuringiensis insecticidal proteins) and its non-transgenic parent variety Simian No.3 at four different growth phrases (seedling,squaring,flowering and boll-forming,and boll-opening).Based on amplification of 16S rDNA retrieved from the soil microbial communities associated with both transgenic and non-transgenic cottons,terminal restriction fragment length poly-morphism (T-RFLP) analysis,clone library construction and sequencing were carried out to see changes in bacterial and archaeal community structures in the soils.Shannon-Wiener index analysis showed that bacterial diversity declined and a certain change occurred in archaeal diversity as well in bulk soil,indicating microbial communities were affected by season succession.According to the clone library and sequencing analysis,the dominant microorganisms in the soil were bacteria and archaea that have never been cultivated or known for their functions in the soil ecosystem.It remains unclear what causes these differences and whether these differences have any ecological threats and bio-risk to the soil ecosystem.Compared to bulk soil samples,the rhizosphere soil samples showed cultivation of cotton varieties remarkably affected bacterial and archaeal communities therein.Variation of bacterial and archaeal communities,especially the archaeal community,was significantly associated with both cotton variety and growth season in T-RFLP analysis,.Since archaeal community is less diversified than bacterial community,the study illustrates that the impacts of transgenic cotton on soil microorganisms varied with the microbial background and transgenic cotton affected the less diversified microbial community more.