The Umitaka spur and the Joetsu knoll in the eastern margin of the Japan Sea off Naoetsu are characterized by a high methane flux accompanied by the formation of methane hydrates. Several sediment cores were obtained from this region during the “Natsushima” NT-06-19 cruise. Various geochemistry analyses were carried out on these samples. ANME-1 and ANME-2 groups of archaea were distinguished by biomarkers. ANME-1 was found from the sediment sample covered by a bacterial mat with the maximum concentration of dissolved methane in pore water. The samples in which ANME was detected are characterized by a remarkably high sulphur content.