Abstract Geochemical analyses of sediments, pore water and headspace gas of the piston cores taken from the eastern part of Ulleung Basin of the East Sea (Japan Sea) were carried out to assess the origin of the sedimentary organic matter and interstitial fluid. Several tephra layers within the core are identified as the Ulleung-Oki (10.1 ka), the Aira-Tanzawa (23 ka) and the Ulleung-Yamato (30.9 ka) tephras. With the exception of these volcanic layers, the cores consist predominantly of muddy sediments that contain >0.5% total organic carbon. Atomic C/N ratios and δ13Corg values suggest that the organic matter originated from marine algae rather than from land vascular plants, whereas Rock-Eval pyrolysis suggests that the organic matter is thermally immature and comes from a land vascular plant (Type III). These conflicting results seem to be caused by the heavy oxidization of the marine organic matter. Sulphate concentration profiles of pore waters show strongly linear depletion (r2 > 0.97) with sediment depth. The estimated sulphate–methane interface (SMI) depth using the sulphate concentration gradient was nearly 3.5 m below seafloor (mbsf) in the southern part of the study area, and deeper than 6 mbsf in the northern part of the area. The difference in SMI depths is likely associated with the amount of the methane flux. The methane concentration below the SMI in the two southern cores increases rapidly, implying the occurrence of methanogenesis and anaerobic methane oxidation (AMO). In contrast, the two northern cores have a low methane concentration below the SMI. values measured from all cores were in the range of −83.5 to −69.5‰, which suggests that the methane derives from a methanogenic microbe. values become decreased toward SMI, but increased below SMI; therefore, has eventually the minimum value near the SMI. The values are also decreased when the methane concentration is increased. These phenomena support the typical occurrence of AMO in the study area.