Microbial diversity of hydrocarbon in polluted soil and water bodies explains the variability that exists among various species of microorganisms inhabiting such environments. Sources of these pollutions include among others polycyclic hydrocarbons, heavy metals contamination, industrial wastes and the unregulated use of pesticides. No doubt, Niger Delta region is heavily polluted due to unregulated exploration activities of the petroleum prospecting and exploration industries, including the illegal activities of the locals. This has grossly affected the distribution and existence of some species of microorganisms. The survival of microbes in such polluted sites depends largely on their ability to adapt, tolerate and/or degrade these pollutants. The degradation of these hydrocarbons has resulted in the formation of metabolites some of which influences diversity among the indigenous microbial species. There is a significant relationship between the level of contamination and alterations in the microbial community. Decontamination of polluted sites can be used to increase biodiversity. Therefore, biodiversity is influenced by the concentration of the pollutants. The ecotoxicological effect of petroleum pollution is the need for oxygen during degradation of the hydrocarbon. In a reduced oxygen supply, serious ecological damage may take place. Also, the presence of heavy metals and organic compounds may enhance toxicity to microorganisms.