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The Phapon gold deposit is located in the northern Laos and the northern segments of the Luang Prabang–Loei metallogenic belt. The lode-gold orebodies consist of auriferous calcite veins in the middle, and the surrounding siderite alteration and hematite alteration zones in red color. This deposit is hosted in Lower Permian limestone and controlled by a NE-trending ductile–brittle fault system, and it is characterized by the wallrock alteration of carbonatization and lack of quartz and metal sulfides. The hydrothermal calcite from auriferous calcite veins and red alteration zone, as well as the wall rocks of limestone and sandstone were selected for rare earth elements (REE) and C–O isotope analyses. The two types of calcite and limestone have generally consistent REE patterns and δEu and δCe values, which are completely different from those of sandstone. Calcites from the auriferous vein show slight light rare earth elements (LREE)-depleted patterns and higher Tb/La and Sm/Nd ratios than the ones from the red alteration zone with slight LREE-enriched patterns. These values indicate that the calcites from the auriferous veins and the red alteration zones are products of homologous fluids, but the former ones are generally likely to form later than the latter ones. The hydrothermal calcites have C–O isotope compositions within the range of marine carbonate, and markedly different from the magmatic or mantle reservoir values. Taking the Y/Ho–La/Ho and Tb/Ca–Tb/La variations into consideration, we believe the hydrothermal calcites could be formed from remobilization and recrystallization of the ore-hosted limestone, and the fluid-wallrock interaction played a major role in the gold mineralization in Phapon. In combination with the regional and local geology, the ore-forming process is suspected to be primarily associated with dehydration and decarbonisation of the Lower Permian limestone and Middle–Upper Triassic sandstones. The Phapon gold deposit could have been formed during the Late Triassic–Jurassic regional dynamic metamorphism driven by Indochina–Sibumasu post-collisional magmatism. A number of features in Phapon are similar to epizonal orogenic deposit, but it is still a unique calcite vein type gold deposit in the Luang Prabang-Loei metallogenic belt.