<p>Methane hydrate samples were collected during the KS-25-8 cruise from three sites in the back-arc basin located offshore western Honshu, Japan: NW Torigakubi Spur (TRKB), NE Rokko-Oki Uplift Zone (ROUZ), and SW Oki Ridge (OR). Massive methane hydrates recovered from piston cores were analyzed for gas compositions and isotope ratios (δ¹³C-CH₄ and ³He/⁴He) to investigate methane origin and contributions of mantle and crustal fluids. Gas compositions are dominated by methane with contributions from ethane and higher hydrocarbons. Carbon isotope compositions of methane (δ¹³C-CH₄ = − 69.8‰ to − 37.5‰) indicate that thermogenic methane occurs at the NW TRKB, whereas microbial methane predominates in the NE ROUZ and SW OR. Methane is predominantly derived from shallow microbial and thermogenic sources, whereas mantle-derived methane contributes less than 0.1% of the total methane. Measured ³He/⁴He ratios range from 0.95 to 1.34 Ra (Ra is the ³He/⁴He ratio of air; 1.39 × 10^− 6), and ⁴He/²⁰Ne ratios range from 0.41 to 1.13, exceeding the atmospheric value (⁴He/²⁰Ne = 0.318). No clear evidence of degassing-related depletion of light noble gases (He and Ne) is observed. After correction for atmospheric contamination, the corrected ³He/⁴He ratios (Rc) range from 0.93 to 1.51 Ra. The elevated ³He/⁴He and high ⁴He/²⁰Ne ratios indicate the presence of a mantle-derived helium component contributing 10–20% of the non-atmospheric helium (crust and mantle). The mantle-derived helium implies the presence of permeable fault systems through which mantle fluids may migrate toward the shallow subseafloor sediments. These results provide geochemical evidence for mantle fluid migration in an extinct back-arc basin.</p>