Consistent patterns concerning distribution of hydrocarbon oxidizing and sulphate reducing bacteria in water and sediments of Absheron littoral of Caspian Sea has been established as a result of three years investigations. The key factors determining the functional activity of these processes were revealed. Obtained results have demonstrated the potential hazard of hydrocarbon contamination of littoral due to formation of a local anaerobic zone both, in water column and sediments; which may lead to sharp development of sulphate reducing microorganisms and the hydrogen sulphide deposition.