Hydrate-bearing sediment cores were retrieved from the Joetsu Basin (off Joetsu city, Niigata Prefecture) at the eastern margin of the Japan Sea during the MD179 gas hydrates cruise onboard R/V Marion Dufresne in June 2010. We measured molecular and stable isotope compositions of volatiles bound in the gas hydrates and headspace gases obtained from sediments to clarify how the minor components of hydrocarbons affects to gas hydrate crystals. The hydrate-bound hydrocarbons at Umitaka Spur (southwestern Joetsu Basin) primarily consisted of thermogenic methane, whereas those at Joetsu Knoll (northwestern Joetsu Basin, about 15 km from Umitaka Spur) contained both thermogenic methane and a mixture of thermogenic and microbial methane. The depth concentration profiles of methane, ethane, propane, CO2, and H2S in the sediments from the Joetsu Basin area showed shallow sulfate–methane interface (SMI) and high microbial methane production beneath the SMI depth. Relatively high concentrations of propane and neopentane (2,2-dimethylpropane) were detected in the headspace gases of the hydrate-bearing sediment cores obtained at Umitaka Spur and Joetsu Knoll. Propane and neopentane cannot be encaged in the structure I hydrate; therefore, they were probably excluded from the hydrate crystals during the structure I formation process and thus remained in the sediment and/or released from the small amounts of structure II hydrate that can host such large gas molecules. The lower concentrations of ethane and propane in the sediment, high δ13C of propane and isobutane, and below-detection normal butane and normal pentane at Umitaka Spur and Joetsu Knoll suggest biodegradation in the sediment layers.