Detailed geological mapping of a highly fractured Paleozoic (pre-Permian) basement and the scarce outcrops of overlying Permian–Mesozoic cover in the surroundings of the Duje Valley (Picos de Europa Unit, Cantabrian Mountains, NW Spain), together with new field data, have allowed the separation of four genetic fault sets in a polyorogenic area, affected by the Variscan and Alpine cycles. These fault sets are, from oldest to youngest: Variscan thrusts (late Carboniferous), late Variscan strike-slip faults (late Carboniferous–earliest Permian), Alpine normal faults (Permian–Mesozoic) and Alpine reverse faults (Cenozoic). A structural analysis is reported here, based on the joint use of geometric, kinematic and deformational features, cross-cutting and tectono–sedimentary relationships between the structures. This analysis has allowed the recognition and full characterization of the four fault sets. These types of structural analyses are useful for unravelling complex tectonic histories in regions where massive limestone lithologies make reconstructing the timing of fault activity difficult, especially if the basement is affected by late deformation events that are not recorded by cover outcrops.