Methane (CH4) associated with marine and terrestrial sites of serpentinization has been proposed to be abiotic in origin. However, the source of carbon and the depth and temperature of CH4 synthesis often remain inconclusive. We measured the radiocarbon (14C), bulk stable isotope ratios (δ13C and δD) and isotopologue abundance (Δ13CH3D) of CH4, and noble gas isotope composition of gas samples from two hyperalkaline geothermal wells (Happo #1 and Happo #3) at Hakuba Happo, Japan, to constrain the source of carbon and the CH4 generation processes. The CH4 samples from both sites were nearly 14C-free, whereas the carbonate precipitates inside the Happo #1 well contained 14C corresponding to 51 to 62 percent modern carbon, indicating that the majority of CH4 was not generated from the reduction of dissolved carbonate in the hot spring water. CH4 samples from Happo #1 and Happo #3 yielded Δ13CH3D-based apparent temperatures of 206−40+52°C and 323−85+143°C, respectively, which are much higher than the measured well water temperatures (∼50°C). Therefore, 14C and clumped isotopologue temperatures suggest that Hakuba Happo CH4 was generated below the depth where the shallow meteoric water circulated. The 3He/4He ratios were 4.10 and 4.47 Ratm for Happo #1 and Happo #3, respectively. The 3He/4He and 4He/20Ne ratios revealed that approximately 50% of He was of mantle origin, suggesting that the Hakuba Happo hot spring received volatiles, including CO2, from the mantle. However, the observed δ13CCH4 values (approximately −35‰) were significantly lower than those of typical mantle-derived carbon (–5‰), implying that mantle-derived CO2 is not the major carbon source for CH4 formation. High CH4 concentrations in the Hakuba Happo fluids, compared to those in hot springs in the area not associated with serpentinization, suggest that CH4 was generated from 13C-depleted fossil carbon sources and serpentinization-derived H2 at high temperatures (>200°C), and subsequently entrained into the cooler circulating meteoric water system.