We investigate the Jurassic volcanic rocks of the El Quemado Complex in the El Chaltén region (Argentina), which correlate with the youngest eruptive event of the Chon Aike Silicic LIP in southern Patagonia. New zircon crystallization ages of the various silicic units were obtained using U–Pb geochronology measured by in-situ Laser Ablation Inductively Coupled Plasma Mass Spectrometry. The average ages for 12 samples range from 147 to 152 Ma. Xenocrystic zircon cores of Jurassic igneous zircons are characterized by complex cathodoluminescent textures wherein growth surfaces are truncated by dissolution surfaces that are in turn overgrown by euhedral growth zones that exhibit oscillatory magmatic zoning. The cores have a wide range of ages, from 185 Ma to 1.3 Ga. We combine our analyzed xenocryst zircon ages preserved in the El Quemado Complex rhyolites with a compilation of published xenocryst zircon ages documented from Cenozoic to Paleozoic volcanic and plutonic rocks throughout southern Patagonia. The combined datasets suggests three prominent geologic features not currently exposed on the present day surface: (1) widespread abundant Triassic through Permian (200–300 Ma) xenocrystic ages throughout the present day Andean region, which connect to current exposures in Northern Patagonian and that of the Antarctic Peninsula, marking the Paleo-Pacific Gondwanan margin, (2) the existence of widespread Early-Middle Ordovician to Cambrian ages throughout southern Patagonia, and (3) the presence of an old (∼1.0 Ga) crust below that of the Deseado Massif and Tierra del Fuego, which likely extends beneath the present-day Andes.