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The Kvarner area is located in the Northern Adriatic Sea, between the south-east Istrian Swell, the Rijeka coast and the Croatian sea boundary. It includes several islands, representing the outcropping parts of anticlines produced by the compressional/transpressional deformation of the External Dinaric Chain. An extensive 2D seismic dataset, acquired for hydrocarbon exploration and calibrated by wells, allowed us to reconstruct the time structural maps in Kvarner and unravel its regional fault pattern. The Dinaric compressional phase affected the area in the Late Cretaceous, with both thin- and thick-skinned tectonics related to Adriatic Carbonate Platform (AdCP) succession rigidity. Structural highs facing the Kvarner offshore from the Istrian inland continue through the Kvarner and Rijeka bays and outcrop in the islands. These anticlines, originating from the pre-Messinian Dinaric thrust system, were reactivated by the post-Messinian transpression, as testified by flower structures. Several sharp valleys represent two main low structural lineaments, developed between the anticlines and partially incised during the Messinian. They were observed throughout the entire studied area, specifically in the western part of the bays, where the lineament continues through the valleys and penetrates the SW-Istria land. Data show that the Messinian erosional effect and sedimentation patterns were influenced and driven by the morphology of older structures produced by the Dinaric compressional phase.