Rift-related magmatism in the northernmost Gulf of California and the adjacent subaerial Salton Trough and Cerro Prieto basins comprises intermediate to rhyolitic surficial and buried lava flows and domes, including their xenolith cargo. In addition, geothermal drill wells frequently penetrate subsurface gabbroic to granitic sills and dikes, which intruded into Colorado River delta fluviatile and lacustrine sediments. Combined single-crystal U-Th-Pb and (U-Th)/He zircon ages reveal late Pleistocene to Holocene eruption ages for three volcanic centers in adjacent rift basins (from N to S): Salton Buttes (eruption age: 2.48 ± 0.47 ka; 95% confidence), Cerro Prieto (maximum eruption age: 73 ± 7 ka), and Roca Consag (eruption age: 43 ± 6 ka). U-Th zircon and allanite crystallization ages are close to the eruption ages, with the exception of Roca Consag lava, the zircon population of which is dominated by zircon with ca. 1 Ma crystallization ages, a population interpreted to be recycled from an unknown crustal source underlying the Wagner basin. Nd isotopic ratios for subsurface microgabbros from Cerro Prieto (εNd = +8.9) overlap with values for mid-oceanic-ridge basalts (MORB) from the East Pacific Rise, adjacent to the southern Gulf of California. Cerro Prieto microgranites and Salton Sea basaltic xenoliths have similarly elevated εNd values. The lowest εNd value for late Pleistocene–Holocene igneous rocks from the northern Gulf of California is for Cerro Prieto dacitic lava (εNd = +0.6). This value implies minor (<20%) assimilation of continental crustal rocks, which, however, is an upper limit because of crystal-scale evidence for magma contamination by unconsolidated sediment at the time of eruption. Zircon crystals in felsic rocks (rhyolite lavas, intrusive microgranites, and granophyre xenoliths) have trace-element and submantle δ18O compositions that are robust indicators for a mafic source that has exchanged oxygen by interacting with meteoric hydrothermal fluids. Collectively, these data imply that oceanic rifting has initiated in the Salton Trough and Cerro Prieto basins. There, MORB-type magmas formed mafic intrusions within thick sedimentary basin fill, where they became exposed to deep-reaching hydrothermal fluids. Diverse intermediate- to high-silica rhyolitic magmas that are prevalent at the surface are produced by fractional crystallization of mafic parental magmas with minor assimilation of sediments or pre-rift basement rocks, and by partial melting of hydrothermally altered mafic intrusions.