The continental rifting that precedes the breakup of a continent and the formation of a new ocean basin is one of the key processes of plate tectonics. Although often viewed as a two-dimensional process, rifted margins exhibit significant variations along strike. We document along-strike variations developed during the ca. 200–160 Ma continental rifting that formed the margins of the Gulf of Mexico ocean basin. Rayleigh-wave ambient noise tomography reveals a zone of high and low seismic velocity resembling large scale geologic boudins in the mantle lithosphere of the northwestern Gulf of Mexico margin. These features become progressively less prominent eastward following the transition from a magma-poor to a magma-rich passive margin. We infer that mantle refertilization and thickness of the pre-rift lithosphere control deformation style and the along-strike variations in continental rifting. Our results also suggest that deformation during rifting produces long-lived features that persist long after breakup and, therefore, can be used to study rifted margins globally.