Two ~1000 cm long sediment cores were recovered from the Sea of Marmara, one with the occurrence of gas hydrates in the Western High, and the other without hydrates in the Cinarcik Basin. Differences in mineralogical and chemical compositions have been identified between the two sediment cores. Based on the results of the mineralogical and geochemical analyses, the main sources of the sediments are quite similar for both investigated areas, but the authigenic components are different, particularly iron sulfides and carbonates. Authigenic Fe(II) carbonate are much higher in Core MRS-CS-05 in the Western High, while crystalline Fe(III) phases are more abundant in Core MRS-CS-16 in the Cinarcik Basin. Notably, the enrichments of greigite (Fe3S4), a metastable ferromagnetic iron sulfide mineral and intermediate polysulfide, as well as iron carbonates are identified at 400 cmbsf with the maximum iron content in Core MRS-CS-05. These indicate the presence of a more reducing and acidic environment in the Western High, mainly due to higher organic matter content and seepage of heavy hydrocarbons in the sediments.