The most important questions to be answered in the studies regarding the diversity of microorganisms in natural ecosystems are the functions of bacterial communities and how the compositions of these communities are affected by environmental changes. In order to answer these questions, there needs to be conducted advanced studies concerning the community structure. The total bacteria community studies require a huge amount of genetic data and high range of genetic diversity. Molecular techniques are quite valuable in researching the structure and diversity of bacterial communities. To combine various complementary molecular techniques is a nice strategy to keep track of microbial community changes in natural ecosystems. Combining some commonly-used techniques, i.e. polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), molecular cloning and fluorescence in situ hybridization (FISH), this review evaluates the advantages of using these techniques together in determining microbial diversity in environmental samples.