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This chapter provideS an overview of the use of molecular techniques in the analysis of the structure and activity of microbial community in soils. Although the use of genetically engineered microbes or recombinant DNA continues as an important consideration in environmental risk assessment, this topic is secondary and is considered as inclusive in the overall applications of molecular techniques to the analysis of the soil microbiota. In the cell separation method, it was found that an acidic 0.1 M phosphate bufferwith SDS gave higher recovery of bacteria from soils and sediments than Winogradsky salt solution or other phosphate buffers that have been used for extraction from soils and sediments. The need for applications of molecular techniques, such as gene-probing methods, and their specificity have been documented for studies on plasmid transfer in soil populations of Rhizobium.