The southern and central Andes reflect significant along-strike differences of tectonic activity, including shortening, alternating flat-to-normal subduction styles and magmatism. In northern Patagonia, the subduction/supra-subduction system, fore arc, arc and back arc basins developed in an extensional setting during the Paleogene. This was accompanied by landward migration of calc-alkalic magmatism which changed to synextensional bimodal volcanism of rhyolitic ignimbrites and interbedded tholeiitic and alkalic basalts. These Paleogene events occurred during a time when the Farallon–Aluk active ridge reached the South American plate, and the Farallon plate subduction was interrupted. They represent a new tectonic regime, characterized by a transcurrent plate margin. The presence in the back arc of a rigid lithospheric block of 100,000 km2 represented by the North Patagonian Massif focused the rotation of the coastal blocks. This resulted in the development of two Paleogene extensional regions to the north and south, respectively, of the Massif and replaced the former back arc. Plate rearrangement caused by the inauguration of the Nazca plate and its regime of orthogonal subduction at the beginning of the Miocene, re-established typical calc-alkaline arc magmatism at the former upper Cretaceous arc locus. Present seismic activity in the subducted plate and tomographic modeling of p-wave velocity anomalies in the upper mantle also suggest the presence of a subduction gap that lasted for most of the Paleogene in northern Patagonia.