Multichannel seismic reflection images across the transition between the east Alborán and the Algero‐Balearic basins show how crustal thickness decreases from about 5 s two‐way traveltime (TWTT, ∼15 km thick) in the west (east Alborán basin) to ∼2 s TWTT typical of oceanic crust (∼6 km thick) in the east (Algero‐Balearic basin). We have differentiated three different crustal domains in this transition, mainly on the basis of crustal thickness and seismic signature. Boundaries between the three crustal domains are transitional and lack evidence for major faults. Tilted blocks related to extension are very scarce and all sampled basement outcrops are volcanic, suggesting a strong relationship between magmatism and crustal structure. Stratigraphic correlation of lithoseismic units with sedimentary units of southeastern Betic basins indicates that sediments onlap igneous basement approximately at 12 Ma in the eastern area and at 8 Ma in the western area. Linking seismic crustal structure with magmatic geochemical evidence suggests that the three differentiated crustal domains may represent, from west to east, thin continental crust modified by arc magmatism, magmatic‐arc crust, and oceanic crust. Middle to late Miocene arc and oceanic crust formation in the east Alborán and Algero‐Balearic basins, respectively, occurred during westward migration of the Gibraltar accretionary wedge and shortening in the Betic‐Rif foreland basins. Arc magmatism and associated backarc oceanic crust formation were related to early to middle Miocene subduction and rollback of the Flysch Trough oceanic basement. Subduction of this narrow slab beneath the Alborán basin was coeval with collision of the Alborán domain with the Iberian and African passive margins and subsequent subcontinental‐lithosphere edge delamination along the Betic‐Rif margins.