The Trans-Altai Zone in southern Mongolia is characterized by thrusting of greenschist-facies Silurian oceanic rocks over Devonian and Lower Carboniferous volcano-sedimentary sequences, by E–W directed folding affecting the early Carboniferous volcanic rocks, and by the development of N–S trending magmatic fabrics in the Devonian–Carboniferous arc plutons. This structural pattern is interpreted as the result of early Carboniferous thick-skinned E–W directed nappe stacking of oceanic crust associated with syn-compressional emplacement of a magmatic arc. The southernmost South Gobi Zone represents a Proterozoic continental domain affected by shallow crustal greenschist-facies detachments of Ordovician and Devonian cover sequences from the Proterozoic substratum, whereas supracrustal Carboniferous volcanic rocks and Permian sediments were folded into N–S upright folds. This structural pattern implies E–W directed thin-skinned tectonics operating from the late Carboniferous to the Permian, as demonstrated by K–Ar ages ranging from ~320Ma to 257Ma for clay fractions separated from a variety of rock types. Moreover, the geographical distribution of granitoids combined with their geochemistry and SHRIMP U–Pb zircon ages form distinct groups of Carboniferous and Permian age that record typical processes of magma generation and increase in crustal thickness. The field observations combined with clay ages, the geochemical characteristics of the granitoids and their ages imply that the E–W trending zone affected by tectonism migrated southwards, leaving the Trans Altai Zone inactive during the late Carboniferous and Permian, suggesting that the two units were tectonically amalgamated along a major E–W trending strike slip fault zone. This event was related to late Carboniferous subduction that was responsible for the vast volume of granitoid magma emplaced at 300–305Ma in the South Gobi and at 307–308Ma in the Trans-Altai Zones. The formation and growth of the crust was initially due only to subduction and accretion processes. During the post-collisional period from 305 to 290Ma the addition of heat to the crust led to the generation of (per-) alkaline melts. Once amalgamated, these two different crustal domains were affected by N–S compression during the Triassic and early Jurassic (185–173Ma), resulting in E–W refolding of early thrusts and folds and major shortening of both tectonic zones.