Vertical profiles of dissolved methane (CH4) and its carbon isotope ratio (13C/12C or 13C) as background values were measured from surface to bottom for the first time in the three major basins of the Japan Sea (East Sea): eastern Japan Basin, Yamato Basin, and Ulleung Basin. Seawater samples were taken using a CTD-Carousel multi-sampling system during the R/V Tansei Maru KT-07-24 cruise in 2007 as a Japan-Korea collaborative study. CH4 concentration and its 13CPDB were measured using a CF-IRMS at Hokkaido University. While the CH4 concentrations of surface seawater are 2.6-2.9 nmol kg-1 (13C: -48‰), those at 30-150 m depths show a distinct maximum with the concentration of 4.1-8.5 nmol kg-1 (with the minimum 13C value of -57‰), indicating in situ microbial CH4 production in some anoxic microenvironments. Below the subsurface maximum, CH4 decreases with depth toward a minimum value of about 1 nmol kg-1 at ~1,500 m depth. Then CH4 gradually increases toward the bottom (especially in the Yamato and Ulleung Basins), accompanied by a decrease of the 13C, suggesting biogenic CH4 supply from bottom sediment. Differences in the CH4 and its 13C profiles are recognized among the three basins, probably reflecting a balance between the CH4 consumption and the CH4 flux from seafloor, in association with the abyssal seawater circulation.