The complex crustal structure of the boundary zone between the Iberian and European plates, from the western Pyrenees to the Cantabrian Mountains, is probed by three-dimensional (3-D) gravity and magnetic modeling constrained by deep seismic profiles. The 3-D modeling results support the presence of a continuous Iberian crustal root and suggest that the geometry of the orogenic belt that formed in latest Cretaceous-Tertiary times along the northern margin of Iberia was conditioned by oblique structures separating areas characterized by different tectonic styles. In the western Pyrenees and the Basque-Cantabrian basin (a thick Mesozoic basin presently incorporated to the Pyrenean-Cantabrian belt), the relatively narrow thinning of the crust inherited from the Mesozoic rifting stage conditioned a structural style in which portions of the southward indenting European lower crust are interpreted to be back thrusted toward the north and uplifted to shallow depths, promoting the appearance of significant potential field anomalies. In the Basque-Cantabrian basin, the strongest aeromagnetic anomaly of the whole Iberian Mainland is superimposed on the eastern part of a well-defined positive gravity anomaly, similar in amplitude and wavelength to those located along the North Pyrenean Zone. These observations suggest that the eastern part of the dense, lower crustal causative body is strongly magnetized and may correspond to a gabbroic cumulate originated in the axis of the ancient Mesozoic rift. To the west, Tertiary compression affected the North Iberian (Cantabrian) passive continental margin, whose geometry and inherited structures conditioned the formation of a double crustal delamination and the uplift of the Cantabrian Mountains.