—The Lugokanskoe deposit is located in southeastern Transbaikalia and has been studied for a long time by many researchers. However, the type of its formation is still debatable. In this paper we study the mineral composition of ores by modern methods, recognize and describe the main gold mineral assemblages, and present detailed data on the chemical composition of native gold and sulfide minerals and their isotope composition. We have established that gold–pyrite–chalcopyrite–arsenopyrite and gold–bismuth parageneses localized in skarn deposits are the main productive assemblages. Study of the sulfur isotope composition of sulfide minerals has shown an endogenous source of sulfur of the ore minerals. The carbon and oxygen isotope compositions of carbonates of ore-bearing veins indicate the participation of a magmatic fluid. The established age of the gold mineralization and igneous rocks of the Shakhtama complex, together with direct geological observations, points to their spatial, temporal, and genetic relationships. According to their petrochemical and geochemical characteristics, the igneous rocks of the Shakhtama complex are I-type ilmenite (reduced) granitoids. Study of fluid inclusions by heating and cooling and Raman spectroscopy has shown that the mineral formation was accompanied by a gradual decrease in the content of salts in the ore-forming fluids and by a decrease in their homogenization temperatures. Optical observations demonstrate that the fluid was heterogeneous at the early stages of the mineral formation. The evolution of the ore system was accompanied by a change in the gas phase composition of fluid inclusions from predominantly nitrogen–carbon dioxide to essentially aqueous, with carbon dioxide impurity (H2O + CO2 ± N2 → H2O ± CO2). The research data testify to the magmatic nature of fluids and the participation of meteoric waters at the late stages of the ore-forming process. The data obtained have led to the conclusion that the Lugokanskoe gold deposit is related to reduced intrusions formed at a shallow depth.