Earlier, a belt of alkali-granite plutons and a carbonatite province were discovered in the South Gobi Desert, Mongolia. The Lugingol pluton of pseudoleucitic syenites with carbonatites was assigned to the alkali-granite belt. However, new dating showed that it is 40 Myr younger than the Khan-Bogdo pluton and a large fault separates it from the alkali-granite belt. In the same part of the South Gobi Desert, a dike series of alkaline K-shonkinites with a rare-metal carbonatite vein was found by V.I. Kovalenko west of the Lugingol pluton, near Mt. Baruun Hasar Uula, and a dike series of alkali and nepheline syenites was found by us northeast of the Lugingol pluton. These data give grounds to distinguish an intrusive complex of K-alkaline shonkinites and leucitic syenites with Late Paleozoic REE-bearing carbonatites. Thus, three alkaline-rock complexes of different ages are distinguished in the South Gobi Desert. We present refined geological maps of these complexes. The plutons of all three complexes are deposits of trace elements (REE, Nb, Zr, Y, P). The chemical composition of the silicate rocks of the complex, rare-metal agpaitic pegmatites, and carbonatite and apatite rare-metal ores was considered in detail. Shonkinites from Mt. Baruun Hasar Uula and the Mountain Pass mine (United States) and their carbonatites, along with the Lugingol carbonatites, belong to a single association of K-alkaline rocks and carbonatites, as evidenced by their identical chemical, mineral, and geochemical rare-metal compositions. Rare-earth element patterns and spidergrams show similarities and differences between the rare-metal rocks of three complexes as well as paragenetic differences between their rare-metal minerals. A rare process is described—the amorphization of rare-metal minerals, related to their high-temperature crystallization in a medium with abnormal silica contents of the Khan-Bogdo pegmatites. The parental magmas of the alkali-carbonatite complexes were generated from the EM-2 contaminated mantle that had undergone recycling, whereas the parental magmas of the Khan-Bogdo agpaitic alkali granites were produced from depleted mantle.