The structure of the southeastern Gulf of California rifted margin is only partly known because of the thick sedimentary cover of the continental shelf and coastal areas of Sinaloa and Nayarit. Here we report the subsurface structure and probable age of the Mazatlán basin, one of the largest buried basins, based on interpretation of reprocessed by multichannel 2D reflection seismic profiles and an exploratory well drilled by Petroleos Mexicanos (PEMEX) between 1979 and 1980, as well as gravimetric data. The Mazatlán basin is located just north of the active subduction zone of the Rivera plate and west of the new oceanic crust accreted since the Pliocene at the mouth of the Gulf. The basin is bounded to the west by a high of the Late Cretaceous batholiths exposed in the Tres Marias Islands and in the normal faults bounding the Nayarit Troughs, and to the east by the late Oligocene-early Miocene extensional faults bounding the Sierra Madre Occidental. Based on the characteristics of the seismic profiles, the basin can be divided into three main sectors. The transition between the northern and central sectors is defined by an abrupt deepening of the basement that corresponds to the westward prolongation of ENE-WSW trending accommodation zones separating opposite tilted domains in the Sierra Madre Occidental. The acoustic basement is clearly defined in the central sector by a set of high-amplitude reflectors suggesting an igneous origin. The deepest part of the basin is located toward the coastal plain of Nayarit and coincides with a gravimetric minimum. We identify several high amplitude reflectors interpreted as mafic sills, which become more abundant toward the south. At least part of them can be correlated with the widespread mafic volcanism emplaced at 9–12 Ma along the eastern margin of the Gulf of California rift. In the northern and central sectors we identified three main stratigraphic boundaries (L1, L2, and L3) within the basin filling, which define seismo-stratigraphic sequences. The shallower sequences, limited by the L1 and L2 boundaries and attributed to the Pleistocene and part of the Pliocene, lack evidence of significant deformation. The sequence above L3 boundary, can be assigned to the earliest Pliocene and the Miocene since they are intruded by a ~ 10 Ma basaltic sill cut by the Huichol-1 exploratory well. The lower part of the basin is characterized by high amplitude reflectors that pinches out against the acoustic basement and correspond to volcanic tuffs and sedimentary deposits correlative with the lower member of the Comondú group exposed in Baja California, which includes ~23 to ~19 Ma distal part of ignimbrites sourced from the Sierra Madre Occidental in Nayarit. Faults with the most significant displacements have a listric geometry and dip from the E to NE. The maximum sediment thickness reported in the Huichol-1 well is 2800 m, with a two-way travel time of 2.7 s, but it reaches 3.7 TWTT in some areas. Based on sedimentation rates, the minimum age for the onset of sedimentation in the basin is ~19 Ma, which is consistent with the regional tectonic evolution of the margin.