The gas geochemistries of high-temperature and low-temperature hydrothermal fluids (HTHFs and LTHFs, respectively) were studied for the Suiyo Seamount hydrothermal system (140°39′E, 28°33′N) in the southern Izu-Bonin (Ogasawara) Arc of the western Pacific Ocean. HTHFs (290 ± 20°C) were collected from four active vents using a gas-tight fluid sampler, which prevented the loss of volatile components through degassing during sample processing. The end-member CH₄ concentrations were homogeneous across the vent fields. LTHFs were collected from four diffuse flow zones using a funnel, which was deployed on the seafloor with replacement of the seawater inside the funnel by the LTHF. Strong linear relationships were found among the concentrations of CH₄, ΣCO₂, and Si of the obtained samples, which ensured that the end-member chemical composition of the LTHFs could be accurately estimated. While the ΣCO₂ concentrations of the HTHFs and LTHFs were similar, all four LTHFs showed enrichment of CH₄ as compared to the HTHFs. The carbon isotopic composition of CH₄ also revealed a significant difference: the LTHFs (δ ¹³C(CH₄) = −4.8 ± 0.3‰PDB) showed ¹³C enrichment, as compared to the HTHFs (δ ¹³C(CH₄) = −5.8 ± 0.4‰PDB). The ¹³C enrichment can be explained by a combination of microbial CH₄ production and oxidation after formation of the LTHFs. On the basis of the observed differences in CH₄ concentrations and carbon isotopic compositions of the HTHFs and LTHFs, microbial methane oxidation and production are estimated to have comparable impacts. These results support the notion of a subseafloor microbial consortium of methanogens and methanotrophs.