The evolution of the North Aegean Sea is studied through the development of three deep basins: the North Aegean Trough, the North Skyros Basin and the Ikaria Basin. Bathymetric data, a 2D seismic dataset and the well-investigated stratigraphic records of the onshore deep basins of northern Greece and Western Turkey were used to make structural and seismic stratigraphic interpretations. The study area shows two sharp unconformities that correspond to the Eocene-Oligocene transition and the Miocene-Pliocene shift. These discontinuities were used as marker horizons for a more detailed structural and seismic stratigraphic interpretation resulting in the identification of several seismic units. A general seismic signature chart was established using onshore basin stratigraphy and well data, which was then used to constrain the ages of the different seismic units. The main features observed in the basins are interpreted as: 1) trans-tensional growth patterns in Pliocene and Quaternary sediments that combine NE–SW trending and steeply dipping fault zones that likely correspond to strike-slip corridors and E-W/WNW-ESE trending normal faults, 2) regional erosional truncations of Miocene sediments, likely related to the Messinian Salinity Crisis (MSC), 3) thick delta-turbidite deposits of Neogene age. Only the North Aegean Trough shows evidence of earlier development and polyphase deformation through inversion structures, and additional seismic units. Extension processes in the Aegean region have been driven by the Hellenic slab rollback since the middle Eocene. The widespread development of Neogene basins at the whole Aegean scale attests to a major tectonic change due to an acceleration of the trench retreat in the middle Miocene. The present study shows that the Neogene basins of the North Aegean Sea developed in dextral transtension with the northward migration of the associated NE-SW trending strike-slip faults. At regional scale, this tectonic pattern indicates that the westward escape of Anatolia started to interact with the trench retreat in the middle Miocene, around 10 Myr before the arrival of the North Anatolian Fault in the North Aegean Sea.