The geologic record of the formation of marine basins during continental rifting is uncommonly preserved. Using GIS-based paleotectonic maps, we show that marine basin formation in the Gulf of California–Salton trough oblique rift (Mexico and the United States) occurred in a stepwise manner as crustal thinning lowered elevations within the Gulf of California Shear Zone, and subsidence along strike-slip and transtensional faults linked isolated pull-apart basins. At 8 Ma, the earliest marine conditions in the Gulf of California were restricted to an embayment at its southern mouth. Farther north, the plate boundary was a set of continental strike-slip faults and linked pull-apart basins, similar to the modern Walker Lane in Nevada and California. By ca. 7 Ma, a series of marine incursions breached across strike-slip faults to the Pescadero and Farallon basins. Marine waters then breached a 75–100 km-long transtensional fault zone between the Farallon and Guaymas basins, with intermittent flooding that led to accumulation of extensive evaporite deposits in the Guaymas basin. Marine incursion north of the Guaymas basin via breaches across the Guaymas and Tiburón strike-slip faults and transtensional zones resulted in flooding of the northern >500 km of the oblique rift by 6.5–6.3 Ma. Thus, strike-slip and transtensional faulting promoted localization of plate boundary strain and guided punctuated marine flooding of the Gulf of California seaway. Inception of the narrow, 1500-km-long Gulf of California at ca. 6.3 Ma was followed by complete continental rupture in the Guaymas basin at ca. 6.0 Ma.