Detailed interpretation of multi-channel seismic reflection profiles showed that the deposition of the Miocene successions in the Cilicia–Adana basin complex occurred within a foredeep, south of the arcuate Tauride fold–thrust belt. The Misis–Kyrenia fault zone defined the northernmost of a number of smaller thrust culminations developed within this foredeep. Fluvio-deltaic successions suggest that the Adana and Inner Cilicia basins became emergent during the Tortonian, when the western portion of the piggy-back basin retained a marine connection. The entire region became emergent during the Messinian salinity crisis, and up to 1000 m of evaporites were deposited in the Cilicia and southern Adana basins. Stratigraphic and structural relationships demonstrated that the late Plio-Quaternary Cilicia–Adana basin complex evolved as an asymmetric piggy-back basin on the hanging wall of the large south-verging Misis–Kyrenia thrust culmination. On the Misis–Kyrenia segment of the culmination, thrust activity ceased in early Messinian, whereas on the Kyrenia segment, it continued to the present. The shift in the kinematics is expressed by the development of the NE–SW trending steep faults with extensional separations bounding the Plio-Quaternary depocentre in the Adana and Inner Cilicia basins. These basement-rooted faults are incompatible with the contractional regime that existed in this part of the basin complex during the Miocene. In the Outer Cilicia Basin, the incompatibility between a domain of continued south-directed fold–thrust activity and uplift on the Kyrenia Range and a domain of extension associated with the development of Plio-Quaternary depocentre indicates that strain is strongly partitioned across the E–W trending southern basin-bounding fault system along the southern margin of the Outer Cilicia Basin. Progressive westward displacement of the Tauride block within the Aegean–Anatolian microplate created a localised transtensional regime within the Inner Cilicia and Adana basins, suggesting the presence of hard intra-plate fault boundaries centred along the Misis–Kyrenia horst block and the southern basin-bounding fault system. The northern basin-bounding fault system, including the Kozan fault in the Cilicia Basin, is a set of large antithetic structures linked to the master faults. The westward pull-out of the Tauride block is related to the overall westward escape of the Aegean–Anatolian microplate during the latest Miocene to early Pliocene, whereas the continued contraction south of the basin complex across Cyprus is related to the evolving collision and under-plating of the continental micro-fragment, the Eratosthenes. We propose that the southern master fault of the Outer Cilicia Basin primarily functions as a boundary separating a contractional microplate domain to the south from a transtensional microplate domain to the north.