Recent developments in molecular techniques have provided an outstanding opportunity to investigate in situ diversity and activity of bacterial communities in various ecosystems. These techniques are based on the detection of nucleic acids within living cells or after extraction directly from field material. They include several DNA fingerprinting, hybridization and analytical PCR-based techniques. Molecular techniques were designed to circumvent the limitations associated with traditional microbiological methods, which often involved characterization of readily cultivated species. The use of molecular methods has contributed significantly to a comprehensive understanding of the microbiology of ecological systems. The application of molecular techniques to oil-contaminated sediments has provided valuable information on the diversity of oil-tolerant bacteria and the identification of field dominant species that were significantly involved in the degradation of pollutants. This has led to the discovery of numerous novel bacterial species that were not previously described among isolates. Furthermore, using molecular techniques, the activity of oil-degraders could be assessed by following the expression of relevant functional genes. The obtained knowledge has facilitated the selection of appropriate microorganisms and the design of suitable treatments for bioremediation purposes. In bioremediation studies, molecular techniques have served as monitoring tools to follow changes and responses of bacterial communities to a given treatment. Thus, correlations between microbial community compositions and the progress of biodegradation could be determined. Herein we focus on the description of various molecular techniques and give examples of their application in oil biodegradation and bioremediation studies. The advantages as well as the disadvantages of each technique will be discussed so that the reader is well aware of the potential and the problems encountered during the application of these techniques. The main aim is to provide scientists in this field with extra tools to learn more about the role of bacteria in the cleanup of contaminated sediments. Moreover, this work will enable scientists to choose from these techniques the best suited for their applications.