The key magmatic processes that lead to the formation of large magmatic-hydrothermal porphyry copper mineral deposits remain uncertain, and a particular question is why a few of these deposits, such as the Pebble porphyry Cu-Au-Mo deposit, are strongly enriched in both gold and molybdenum. This study investigated the igneous rocks of the Pebble district and obtained major and trace element compositions, Sr and Nd isotopic compositions, and zircon age and trace element data to model the origin of the ore-forming magmas. The Pebble porphyry Cu-Au-Mo deposit, one of the world’s largest Cu-Au resources, formed during the final stages of regional Late Cretaceous arc magmatism (101–88 Ma) in the Southwest Alaska Range. Local pre-mineral intrusions (99–95 Ma) are dominated by alkaline compositions including monzodiorite stocks, shoshonite dikes, and monzonite porphyries, but also include lesser volumes of high-K calc-alkaline diorite and granodiorite sills. The occurrence of early alkaline magmas has been noted at other gold-rich porphyry systems, including Bingham and Kerr-Sulfurets-Mitchell. Mineralization at Pebble is associated with granodiorite to granite porphyry dikes related to the >165 km 2 high-K calc-alkaline Kaskanak granodiorite batholith (91–89 Ma). Over a period of 10 m.y., Late Cretaceous melts evolved from high temperatures (930–730 °C) and modestly hydrous and oxidized conditions to relatively low temperatures (760–680 °C) and very hydrous and oxidized conditions. Collectively, all Late Cretaceous igneous rocks at Pebble contain magnetite and little or no ilmenite, are metaluminous to weakly peraluminous, and have typical arc trace element enrichments and depletions. They have moderate Sr/Y ratios (20–55) and gently sloped REE profiles (La/Yb = 5–20) that are not adakitic, which supports a source area lacking garnet that is consistent with a thin crust in southwest Alaska. Radiogenic isotopes for Late Cretaceous intrusions at Pebble have a restricted range of primitive Sr and Nd isotopic compositions ( 87 Sr/ 86 Sr i = 0.70329–0.70424; ɛNd i = 4.9–6.1), which overlap with volcanic and plutonic basement rocks of the Jurassic Talkeetna Arc along the Alaska Peninsula. The Kaskanak batholith intrudes the Late Jurassic–Early Cretaceous Kahiltna flysch, and mixing models using Sr and Nd isotopes indicate that the Kaskanak batholith assimilated ≤10 wt% Kahiltna flysch in amounts that did not likely affect magma fertility. Xenocrystic zircon samples are abundant in Cretaceous pre-mineral intrusions and have U-Pb ages similar to detrital zircon samples in the Kahiltna flysch. These data support some assimilation of upper crustal Kahiltna flysch, but the dominance of Devonian–Mississippian xenocrystic zircon populations in some intrusions suggests derivation from unexposed older basement. The extraordinary endowment of Cu and Au at Pebble is inferred to result from primitive calc-alkaline and alkaline arc magmas and the hydrous and strongly oxidized conditions that suppressed the formation and fractionation of Cu- and Au-enriched sulfide melts. Furthermore, differentiation to silicic compositions was a product of extensive crystal fractionation of parental melts accompanied by minor crustal assimilation. The trace element content of the intermediate composition intrusions indicates that both hornblende and titanite fractionation processes in the mid- to shallow-crust were both required to produce the more evolved granodiorite and granite porphyry compositions. Despite the apparent lack of Mo-enriched continental crust in the region, primitive hydrous melts were produced by protracted arc magmatism and were modified by minor crustal assimilation including early alkaline magmatism, periodic recharge of mafic hydrous basalts and hybrid andesites, and fractional crystallization, which was apparently sufficient to enrich Mo in late stage felsic melts.