The Jurassic ophiolites in the South Apuseni Mountains represent remnants of the Neotethys Ocean and belong to the East Vardar ophiolites that contain ophiolite fragments as well as granitoids and volcanics with island-arc affinity. New U–Pb zircon ages, and Sr and Nd isotope ratios give insights into their tectono-magmatic history. The ophiolite lithologies show tholeiitic MOR-type affinities, but are occasionally slightly enriched in Th and U, and depleted in Nb, which indicates that they probably formed in a marginal or back-arc basin. These ophiolites are associated with calc-alkaline granitoids and volcanics, which show trace element signatures characteristic for subduction-enrichment (high LILE, low HFSE). Low 87Sr/86Sr ratios (0.703836–0.704550) and high 143Nd/144Nd ratios (0.512599–0.512616) of the calc-alkaline series overlap with the ratios measured in the ophiolitic rocks (0.703863–0.704303 and 0.512496–0.512673), and hence show no contamination with continental crust. This excludes a collisional to post-collisional origin of the granitoids and is consistent with the previously proposed intra-oceanic island arc setting. The new U–Pb ages of the ophiolite lithologies (158.9–155.9 Ma, Oxfordian to Early Kimmeridgian) and granitoids (158.6–152.9 Ma, latest Oxfordian to Late Kimmeridgian) indicate that the two distinct magmatic series evolved within a narrow time range. It is proposed that the ophiolites and island arc granitoids formed above a long-lived NE-dipping subduction zone. A sudden flip in subduction polarity led to collision between island arc and continental margin, immediately followed by obduction of the ophiolites and granitoids on top of the continental margin of the Dacia Mega-Unit. Since the granitoids lack crustal input, they must have intruded the Apuseni ophiolites before both magmatic sequences were obducted onto the continental margin. The age of the youngest granitoid (~153 Ma, Late Kimmeridgian) yields an estimate for the maximum age of emplacement of the South Apuseni ophiolites and associated granitoids onto the Dacia Mega-Unit.