The prime objective of this approach is to study the impacts of genetically modified crops in the rhizosphere environment, to explore uncultured bacteria. A bacterium is most abundant diverged group of microbes, which are present in the soil. Most of the bacterial species are unable to be cultured under laboratory conditions and diversity is still poorly understood. The molecular approaches can only be used to monitor soil microbial populations that can modulate or contribute directly to soil. This new and exciting molecular method is metagenomics, an extraordinary analysis tool to know the uncultured microbial diversity. Here our aim is to study the bacterial community diversity in a rhizosphere soil before and after inoculation of genetically modified crops by using culture independent techniques - extracting metagenomic DNA from genetically modified Bt cotton crop rhizosphere soil.