The volcanic rocks of the Chon Aike Silicic Large Igneous Province (CASP) are recognized as magmas dominantly produced by crustal anatexis. Investigating the zircon of the CASP provides an opportunity to gain further insight into geochemical and isotopic differences of the potential magmatic sources (i.e., crust versus mantle), to identify crustal reservoirs that contributed to the felsic magmas during anatexis, and to quantify the contributions of the respective sources. We present a combined zircon oxygen and hafnium isotope and trace element dataset for 16 volcanic units of the two youngest volcanic phases in Patagonia, dated here with LA-ICP-MS U–Pb geochronology at ca. 148–153 Ma (El Quemado Complex, EQC) and ca. 159 Ma (western Chon Aike Formation, WCA). The EQC zircon have ¹⁸ O-enriched values (δ ¹⁸ O from 7 to 9.5‰) with correspondingly negative initial εHf values (− 2.0 to − 8.0). The WCA zircon have δ ¹⁸ O values between 6 and 7‰ and εHf values ranging between − 4.0 and + 1.5. Binary δ ¹⁸ O-εHf mixing models require an average of 70 and 60% melt derived from partial melting of isotopically distinct metasedimentary basements for the EQC and WCA, respectively. Zircon trace element compositions are consistent with anatexis of sedimentary protoliths derived from LIL-depleted upper continental crustal sources. The overlap between a high heat flux environment (i.e., widespread extension and lithospheric thinning) during supercontinental breakup and a fertile metasedimentary crust was key in producing voluminous felsic volcanism via anatexis following the injection and emplacement of basaltic magmas into the lower crust.