The Alto Molise area belongs to the Apennine orogenic belt, which has been developing since the Late Cretaceous as a result of the Europe–Africa collision. This area is characterized by the complex superposition of different palaeogeographic domains that developed during the Mesozoic along the passive southern margin of Tethys Ocean. These domains have been subdivided into four main structural units; from shallowest to deepest they are: the Sannio pelagic basin, the Latium-Abruzzi carbonate platform, the Molise pelagic basin and the Apulia carbonate platform Units. Until the present study, the tectonic relationship among these units was thought to have been mainly determined by Early Messinian to Late Pliocene thrusting. This paper reports the results of a new geometric and kinematic analysis of the Alto Molise area. This new interpretation of the Alto Molise structural style indicates that strike-slip tectonics played a primary role during post-Pliocene times, greatly modifying the previous Alto Molise thrust structures. Two main tectonic events are recorded, consisting of the Pliocene thrusting of the Molise domain onto the Apulia platform followed by the post-Pliocene disruption and rotation of the pre-existing compressional structures by N–S-oriented, high-angle, right-lateral strike-slip faults. These faults are manifest in the Apulia platform as narrow shear zones, but propagate towards the surface into wider belts of strike-slip and oblique-slip deformation. We have compared our results with published structural, palaeomagnetic and anisotropy of magnetic susceptibility (AMS) data from the Central Apennines. This comparison suggests that the superposition of the younger strike-slip tectonic deformation on the older fold and thrust structures in the Alto Molise area is consistent with block-rotation of a segmented orogen, applied to the whole Apennine system.