Seismic interpretation of the MARCONI deep seismic survey enables recognition of the upper crustal structure of the eastern part of the Bay of Biscay and the main features of its Alpine geodynamic evolution. The new data denotes that two domains with different Pyrenean and north foreland structures exist in the Bay of Biscay. In the eastern or Basque‐Parentis Domain, the North Pyrenean front is located close to the Spanish coast, and the northern foreland of the Pyrenees is constituted by a continental crust thinned by a north dipping fault that induced the formation of the Early Cretaceous Parentis Basin. In the western or Cantabrian Domain, the North Pyrenean front is shifted to the north and deforms a narrower and deeper foreland basin which lies on the top of a transitional crust formed from the exhumation of lithospheric mantle along a south dipping extensional low‐angle fault during the Early Cretaceous. The transition between these two domains corresponds to a soft transfer zone linking the shifted North Pyrenean fronts and a north‐ to WNW‐directed thrust that places the continental crust of the Landes Plateau over the transitional crust of the Bay of Biscay abyssal plain. Comparison between this structure and regional data enables characterization of the extensional rift system developed between Iberia and Eurasia during the Late Jurassic and Cretaceous and recognizes that this rift system controlled not only the location and features of the Pyrenean thrust sheets but also the overall structure of this orogen.