Zagros is a relatively young and active fold-thrust belt, which has formed due to convergence between the Eurasian and Arabian plates. Magnetotelluric (MT) soundings along a transect were carried out to determine the crustal structure in the collision zone of the two Palaeocontinents. MT data were analysed and modelled using 2-D inversion schemes. The models show clear conductive and resistive domains along the MT profile consistent to a great extent with documented tectonic features and surface geology. The models obtained from the joint inversion of transverse electric and transverse magnetic modes as well as the inversion of the determinant data show similar features along the profile. The new MT results reveal that the transition between two continents at the surface coincides with the western boundary of Sanandaj-Sirjan Zone (SSZ) at the Main Zagros Thrust (MZT). Along the profile towards northeast the conductors at top indicate massive Neogene sediments of the central domain (CD) while the very thick, shallow-located, resistive body (5–25 km thick and 100 km long) beneath is unlikely to be of oceanic affinity, but continental. Another main feature along the profile is the main resistive and conductive parts of the Arabian Plate, which coincide with the tectonic events of High Zagros Fault and Mountain Front Fault. Two highly conductive thick zones are recognized at the southwest part and in the middle of the profile apparently extending to a depth of about 50 km, possibly related to a downward smearing effect due to the presence of thick sedimentary columns in the upper crust. Along the profile, conductive features are recognized at the metamorphic SSZ and Urumieh-Dokhtar Magmatic Assemblage units as well as at CD. Below site 31 along the surface trace of the MZT, the transition between the two continents is distinguished by a complex sequence of conductive and resistive zones both varying laterally as well as vertically. The main difference between the two domains is that the Eurasian Plate seems to be more resistive than the Arabian Plate, although some part of the difference can be related to the thick sequence of conductive sedimentary rocks on the Arabian Plate.