The demographic stories, genetic relationships and population structure of sedentary fish Pomatoschistus marmoratus (Risso, 1810) which are distributed along the eastern basin of the Mediterranean Sea (Including Turkish coasts of the Black Sea, Aegean Sea, Levantine Sea and Sea of Marmara) were investigated by mtDNA COI (652 bp) and Cyt-b (526 bp) regions. It was found that the population groups had high haplotype diversity while the nucleotide diversity was quite low for both gene regions. Phylogenetic analyses of the haplotypes indicated that Levantine population (LEV) were genetically different from other populations and the gene flow between LEV and the other populations was very limited. The results of the analyses of neutrality and mismatch distributions applied to the population groups were evaluated as a whole, it was determined that the BLAMAR group that represents the Black Sea and Sea of Marmara was stable but that the LEV was under the sudden demographic expansion model following the population bottleneck. The genetic variance indices indicated sudden demographic expansion following population contraction were supported by star-shaped haplotype networks. The reason of this limited gene flow and differentiation between the LEV populations and the others are linked with wind-driven offshore transport of the larvae and surface currents in these sub-basins. The timing of the differentiation, demographic stories of populations associated with geological and paleo-climatic events and current ecological conditions were discussed.