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Shallow and deep sources generate a gravity low in the central Iberian Peninsula. Long-wavelength shallow sources are two continental sedimentary basins, the Duero and the Tajo Basins, separated by a narrow mountainous chain called the Spanish Central System. To investigate the crustal density structure, a multi taper spectral analysis of gravity data was applied. To minimise biases due to misleading shallow and deep anomaly sources of similar wavelength, first an estimation of gravity anomaly due to Cenozoic sedimentary infill was made. Power spectral analysis indicates two crustal discontinuities at mean depths of 31.1 ± 3.6 and 11.6 ± 0.2 km, respectively. Comparisons with seismic data reveal that the shallow density discontinuity is related to the upper crust lower limit and the deeper source corresponds to the Moho discontinuity. A 3D-depth model for the Moho was obtained by inverse modelling of regional gravity anomalies in the Fourier domain. The Moho depth varies between a mean depth of 31 km and 34 km. Maximum depth is located in a NW-SE trough. Gravity modelling points to lateral density variations in the upper crust. The Central System structure is described as a crustal block uplifted by NE-SW reverse faults. The formation of the system involves displacement along an intracrustal detachment in the middle crust. This detachment would split into several high-angle reverse faults verging both NW and SE. The direction of transport is northwards, the detachment probably being rooted at the Moho.