This paper focuses on the boundary area between the Central and Southern Apennines thrust belt of the Italian peninsula, which separates two different patterns of distribution of active faults and strong earthquakes along the Apennines chain. In order to reduce the remarkable lack of data on this area, part of this boundary has been investigated. The study area corresponds to the surroundings of the town of Isernia, an important centre of the Molise region, and contains the Carpino and Le Piane (CLP) intermountain Basins of Quaternary age. The research was based on unpublished data, consisting of 65 well logs drilled in the CLP Basins, integrated with detailed field surveys (scale 1:10,000), mesoscale structural analysis and aerial photograph interpretation. This study allowed to define the geometry and kinematics of the CLP Basins. They result to be asymmetric half-grabens partially filled with fluvio-lacustrine deposits, where the sedimentation is controlled by the activity of a set of normal faults striking N30°W and NE dipping. This set of faults, which developed mainly during the Late Pleistocene-Holocene, is about 10 km long and is located close to the northwestern end of the Boiano Basin extensional Fault System. The average slip rate calculated for part of the Holocene for one of the recognised faults ranges from 0.75 to 1.00 mm/year. The identification of the active CLP Basins Fault System partially fills the gap of data at the boundary between the Central and Southern Apennines. From a more general point of view, we hypothesise that this boundary might be regarded as a "persistent segment boundary", forming a long-term barrier to the propagation of rupture of active fault systems. Under this perspective, a redefinition of the seismic zonation of Italy for the study area is suggested.