Surface seawater, collected from three fishing harbors during different seasons of the years 2015, 2016 and 2017, were assessed for physico-chemical analyses. Results showed that seawater was mainly polluted by hydrocarbons and some heavy metals. Microbial communities' composition and abundance in the studied harbors were per-formed using molecular approaches. SSCP analysis indicated the presence of Bacteria, Archaea and Eucarya, with dominance of the bacterial domain. Illumina Miseq analysis revealed that the majority of the sequences were affiliated with Bacteria whereas Archaea were detected at low relative abundance. The bacterial community, dominated by Proteobacteria, Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes, Actinobacteria and Chloro-flexi phyla, are known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbons degradation and heavy metals resistance. The main objectives of this study are to assess, for the first time, the organic/inorganic pollution in surface seawater of Kerkennah Islands harbors, and to explore the potential of next generation marine microbiome monitoring to achieve the planning coastal managing strategies worldwide.