We have investigated the low-temperature history of pre-Neogene basement areas adjacent to the western extension of the North Anatolian Fault zone (NAFZ) by apatite fission track thermochronology of 33 samples taken from Marmara island, Kapidag peninsula (both in the Sea of Marmara), Samothrake island, and Chalkidike peninsula (both in the North Aegean region). Together with already published apatite fission track data from 30 other sampling localities of the region, these data (63 in total) have been evaluated mainly with regard to the transitional period from the Mesohellenic orogeny (Eocene-Oligocene) to the plate-tectonical individualization of the Aegean-Antolian microplate, to gain a better understanding of the tectonical chronology that has led to modern east Mediterranean plate tectonics. Apatite fission track investigations of the area under discussion reveal two major events of cooling and exhumation of pre-Neogene rocks. A first frequency maximum of cooling ages between 35 and 25 Ma (late Eocene to early Oligocene) is due to postorogenic regional erosion after the climax of the Mesohellenic orogeny, which was caused by continental collision of the Pelagonian platform and the Rila-Rhodope zone after the final closure of the Axios-Vardar Ocean. A second frequency maximum of cooling ages between 17 and 11.5 Ma (early to middle Miocene) depicts more localized uplift and exhumation in consequence of transpressive and/or transtensive movements along early structural discontinuities that gave rise to the later fault systems in the western extension of the NAFZ. The earliest fault structures of this system have developed shortly after the orogenic collapse and crustal extension of the Rila-Rhodope area but quasi simultaneously with the onset of subduction along the modern Hellenic trench. The regional distribution of fission track ages of the Miocene age group (17 to 11.5 Ma), and corresponding thermochronological calculations based on frequency distributions of confined track lengths suggest that an early fault propagation has occurred from east to west during the Miocene. The onset of subduction along the Hellenic trench and subsequent gravitational retreat of the subducting oceanic slab are considered as a major cause for transtension of the Aegean crust, especially with regard to the development of north Aegean pull-apart basins. Such early fault structures have facilitated the westward propagation of a continuous NAFZ that took place during the Pliocene from the easternmost Marmara region to the Gallipoli peninsula and to the North Aegean trough.