We have investigated the crustal structure of a 400 km wide zone of thinned continental crust in the northeastern Gulf of Mexico (GOM) using gravity and magnetic modeling along two deeply penetrated seismic transects. Using this approach, we identify two zones of prominent, southward-dipping reflectors associated with 7–10 km thick, dense, and highly magnetic material. Previous workers have interpreted the zones as either coarse clastic redbeds of Mesozoic age that are tilted within half-grabens or seaward-dipping reflectors of magmatic origin. Both seismic reflection lines reveal a 10 km thick and 67 km wide northern zone of high density near the Florida coastline beneath the Apalachicola rift (AR). The southern zone of high density occurs 70 km to the south in the deepwater central GOM along the northern flank of the marginal rift, a 48 km wide, southeast-trending structure of inferred Late Jurassic age that is filled by 3 km of low-density and low-magnetic susceptibility sediments including complexly deformed salt deposits. We propose that these two subparallel rifts and their associated magmatic belts formed in the following sequence: (1) AR formed during Triassic-early Jurassic (210–163 Ma) phase 1 of diffuse continental stretching and was partially infilled on its northern edge by southward-dipping volcanic flows; and (2) the similarly southward-dipping southern magmatic zone formed adjacent to the marginal rift during the early phase 2 of late Jurassic (161–153 Ma) rifting of the GOM continental extension; this southern area of SDR formation immediately preceded the formation of the adjacent oceanic crust that separated the rift-related evaporates into the northern and southern GOM. Our integrated approach combining 2D seismic, gravity, and magnetic data sets results in a more confident delineation of these deep crustal features than from seismic data alone.