Southern Mongolia is part of the Central Asian Orogenic Belt, the origin and evolution of which is not fully known and is often debated. It is composed of several east–west trending lithostratigraphic domains that are attributed to an assemblage of accreted terranes or tectonic zones. This is in contrast to Central Mongolia, which is dominated by a cratonic block in the Hangai region. Terranes are typically bounded by suture zones that are expected to be deep-reaching, but may be difficult to identify based on observable surface fault traces alone. Thus, attempts to match lithostratigraphic domains to surface faulting have revealed some disagreements in the positions of suspected terranes. Furthermore, the subsurface structure of this region remains relatively unknown. Therefore, high-resolution geophysical data are required to determine the locations of terrane boundaries. Magnetotelluric data and telluric-only data were acquired across Southern Mongolia on a profile along a longitude of approximately 100.5° E. The profile extends ~ 350 km from the Hangai Mountains, across the Gobi–Altai Mountains, to the China–Mongolia border. The data were used to generate an electrical resistivity model of the crust and upper mantle, presented here, that can contribute to the understanding of the structure of this region, and of the evolution of the Central Asian Orogenic Belt. The resistivity model shows a generally resistive upper crust (0–20 km) with several anomalously conductive features that are believed to indicate suture zones and the boundaries of tectonic zones. Moreover, their spatial distribution is coincident with known surface fault segments and active seismicity. The lower crust (30–45 km) becomes generally less resistive, but contains an anomalously conductive feature below the Gobi–Altai zone. This potentially agrees with studies that have argued for an allochthonous lower crust below this region that has been relaminated and metamorphosed. Furthermore, there is a large contrast in the electrical properties between identified tectonic zones, due to their unique tectonic histories. Although penetration to greater depths is limited, the magnetotelluric data indicate a thick lithosphere below Southern Mongolia, in contrast to the previously reported thin lithosphere below Central Mongolia.[Figure not available: see fulltext.].