Pronounced differences in age and geochemistry between Cenozoic volcanic rocks within the Salton trough, southern California and northern Baja California, imply their formation within two distinct tectonic settings rather than the previously proposed single phase of continental rifting. The emplacement of Oligocene-Miocene alkaline lavas overlapped with crustal extension and basin formation in the region during this time. Post-4 Ma subalkaline magmatism related to the Gulf of California-East Pacific Rise divergent plate margin exploited crust already ruptured during Miocene extension. New rare earth element and Sr-Nd isotopic data, and K-Ar, 40Ar/39Ar, and U-Pb ages for basalt, andesite, and granophyric granite xenoliths contained within the Salton buttes rhyolite domes, part of the post-4 Ma oceanic spreading regime, indicate that they are the components of a differentiated magmatic system. These data also refute the presence of crystalline basement beneath this part of the Salton trough. We suggest that the rupture of crystalline basement beneath the axis of the Salton trough was more effective during Oligocene-Miocene time.