The Cyprus Arc system constitutes a major active plate boundary in the eastern Mediterranean region. This structure is directly linked with the northward convergence of the African and Eurasian plates since the Late Cretaceous. Two‐dimensional reflection seismic data were utilized, which image the main plate structures and their lateral evolution south of the island of Cyprus. Interpretation of these data allowed the identification of nine tectono‐sedimentary packages in three different crustal domains south of the Cyprus Arc system: (1) the Levant Basin (attenuated continental crust), (2) the Eratosthenes microcontinent (continental crust), and (3) the Herodotus Basin (oceanic crust). Within these domains, numerous tectonic structures were documented and analyzed in order to understand the mechanism and timing of deformation. In the north, south verging thrusting commenced in early Miocene along the Larnaca and Margat ridges, whereas no activity was identified before middle Miocene along the Latakia Ridge. Thus, the deformation front migrated southward and was accompanied by the development of flexural basins and stratigraphic onlaps as in the Cyprus Basin. The acme of deformation occurred in mid‐late Miocene. A regional unconformity of Pliocene age marks the end of the first deformation sequence. In Plio‐Pleistocene time, the westward escape of the Anatolian microplate resulted in the reactivation of existing structures. The evolution of deformation along the plate boundary is identified from the creation of positive flower structures revealing transpressive movements along the Larnaca and Latakia Ridges (eastern domains), whereas in the Eratosthenes domain a flexural basin highlights a compressive regime.