The Seligdar apatite deposit is located in the Aldan-Stanovoy shield of the Siberian platform in Russia. This deposit is a typical ore deposit of the Nimnyrskaya approximately N-S apatite zone, which is about 400 km long. The genesis of the apatite-dolomite ores at the Seligdar deposit is a matter of debate. This article presents new evidence of the carbonatitic genesis of the apatite-dolomite rocks at the Seligdar deposit based on modern methods of mineralogical, geochronological, melt and fluid inclusion investigations. According to our data, the age of the apatite-dolomite ores is 1880 ± 13 Ma (U-Pb SHRIMP, zircon). Study of melt inclusions indicates that the ores were formed from a carbonate melt of dolomitic composition with alkali (sulphates, chlorides and fluorides of Na and K) and silica components (1–10 wt.%) at a temperature of > 1100 °C. The dolomite carbonatites have been subsequently exposed to the intense processes of hydrothermal-metasomatic alteration and metamorphism. The evolution of mineral parageneses from the magmatic apatite-magnetite-dolomite carbonatite stage to the hydrothermal stages with quartz, calcite, monazite-Ce, xenotime-Y, haematite, thorite, thorianite, sulphates and sulphides mineralization agrees with the fluid inclusion regime evolution from the carbonate melt to the chloride brines, and the varying concentrations of the chloride solutions are also described in this article. The investigation of the apatite deposits within the Aldan shield not only allows us to take a new look at the question of their origin but also helps us to study the composition of the ancient mantle, as well as the specifics of apatite-dolomite carbonatite and related hydrothermal Fe and Th-REE mineralization in this region.