The Hishikari gold–silver deposits in southern Kyushu, Japan, are low-sulfidation vein-type epithermal deposits. Bulk composition analysis, fluid inclusion microthermometry and quantitative gas composition analysis on the basis of the crush-fast scan (CFS) method were conducted to elucidate characteristics and behavior of hydrothermal fluids responsible for the gold mineralization of the Hishikari deposits. Quartz vein samples were collected from widely scattered locations of ore veins: Zuisen-6, -3, -1 (Main deposit), Keisen-2 and Shosen-5 (Sanjin deposit), and Seisen-8 (Yamada deposit) between −70 and 64 ML (mine meter level). The samples are composed mainly of quartz and adularia, and ore minerals of electrum, pyrargyrite, pyrite and/or stibnite, having an average bulk Ag/Au weight ratio of 0.54. Fluid inclusions in quartz and adularia are two-phase liquid–vapor, and their trapping temperatures and salinities are ca. 190–220 °C and 1.5–2.7 wt.% NaCl eq., respectively. The salinity is highest with an average 2.4 wt.% NaCl eq. of the fluid inclusions from the deepest level (Zuisen-6 vein at −70 ML), while the fluid inclusion salinities from other samples are relatively low less than ca. 2.0 wt.% NaCl eq. Parallel- and lattice-bladed quartz occur in a number of veins, suggesting fluid boiling during the vein formation. Gases of fluid inclusions are composed mainly of H2O (93.4–99.8 mol%) and CO2 (0.15–6.2 mol%), N2 (0.007–0.96 mol%), Ar (0.0001–0.0047 mol%), CH4 (0.002–0.048 mol%), H2S (0.0004–0.0028 mol%), H2 (0–0.074 mol%) and He (0.0002–0.0011 mol%). CO2, N2 and Ar contents of the fluid inclusions are elevated in the samples collected from deep levels, while H2O, H2S and He contents are elevated in those from shallow levels. The Ar/He, CO2/CH4 and N2/Ar ratios of fluid inclusion gas indicate a systematic transition from magmatic to meteoric signatures in order from deep to shallow levels. The CO2/N2 ratio and volatiles contents are positively correlated suggesting condensation in relatively high Au-grade quartz vein samples (19.5–27.7 ppm Au), while negative correlations suggest boiling with volatile contents less than 1% are indicative of low Au-grade quartz vein samples (0.14 to 0.18 ppm Au). The elevated CO2 contents observed in the Zuisen veins are signatures of the deeply circulating hydrothermal fluid with a magmatic contribution. Due to intermittent boiling of hydrothermal fluid, CO2 and H2S were partitioned into the vapor phase in deeper portions and condensed into the steam-heated meteoric water in shallower portions. The signatures of both meteoric and magmatic fluids in fluid inclusion gas compositions were detected in the samples collected near the unconformity between Shimanto Supergroup (shale and sandstone) and Hishikari Lower Andesite. This suggests that a mixing of the deeply circulating hydrothermal fluids with the steam-heated meteoric water took place near the unconformity, and it was one of the mechanisms to have precipitated gold.