The ocean covers over 70% of the earth’s surface and contains an extraordinary diversity of life. Our interest in understanding the function of marine ecosystems has been accelerated in recent years with growing recognition of their importance in human life. Marine microbes have defined the chemistry of the oceans and atmosphere over evolutionary time. Thousands of different species of bacteria, fungi and viruses exist in marine ecosystems comprising complex microbial food webs. These microorganisms play highly diverse roles in ecology and biochemistry of most different ecosystems. In the preset study, culture independent and dependent approach explored to study the biodiversity of bacterial community of marine ecosystem, which revealed uneven bacterial genera distribution in general, at polluted site of sea coast ecosystem at Alang-Sosiya ship breaking yard. However, in control site of sea water samples, all bacterial genera evenly distributed, which depicts the stability of ecosystem.