Detachment of Baja California peninsula from the North American plate altered the crustal region between them, including extension of the crust between the peninsula and Mexico’s mainland. In the SE portion of this region Bahia de Banderas, a 60-km indentation in the littoral of Mexico, is a boundary region across which significant changes in topography, seismicity, seismic attenuation, trench subduction angle, continental platform width, geomagnetic field, and crustal thickness have been documented. Here we identify two additional, major discontinuities: one in gravity and the second in the regional electrical resistivity to 50-km depth, both associated with the region in which the crust changes from extended to un-extended. Under the former, we ratify and extend the presence of the oceanic slab obtained elsewhere with seismological determinations. Plate rollback is also reported in the boundary region. Gravity and electrical resistivity models locate the NW and SE limits of the rolled-back portion of the oceanic slab; within this region we identify upwelling asthenospheric material. Bahía de Banderas region represents a major tectonic discontinuity, implying the existence of a continental sliver prolonging ~160 km into the San Blas basin north of the bay, the Tres Marías sliver, independent from the Jalisco Block, in which crustal fragmentation processes appear to be still in progress. We argue that this sliver is tectonically different from the Jalisco Block since at least the Late Miocene, when extensional tectonics stretched and thinned its corresponding crust and lithosphere.