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The Kamioka mine, located in Gifu Prefecture in Japan, is famous for the large water Cherenkov detector system, the Super-Kamiokande. The Kamioka skarn-type Pb–Zn deposits are formed in crystalline limestone and are replaced by skarn minerals within the Hida metamorphic rocks. The Kamioka deposits mainly consist of the Tochibora, Maruyama, and Mozumi deposits. The present study focuses on the ore-forming hydrothermal fluid activity in the Kamioka deposits and the peripheral exploration area based on the carbon and oxygen isotope ratios of calcite and rare earth element (REE) analyses. The carbon and oxygen isotope ratios of crystalline limestone (as the host rock) are not homogeneous, and depending on the degree of hydrothermal activity, they decreased to various degrees because of the reaction with the ore fluids. Thus, the carbon and oxygen isotope ratios of crystalline limestone can be used as an indicator of the influence of the hydrothermal fluids for the ore mineralization. The REE contents in the ores of igneous origin are one order of magnitude higher than the limestone origin. Further, depending on the formation temperatures, calcites precipitated during ore mineralization have a stable carbon isotope ratio and a widely varying oxygen isotope ratios. The Kamioka district fracture system is likely a major control factor on ore mineralization from hydrothermal activity. In addition, the skarnization-related ore-forming fluids are mostly meteoric in origin, confirming the conclusions from previous studies. Full article