Based on structural analysis and lithostratigraphic data, as well as geological mapping, the Paleogene part of the Thrace Basin (THB) in NE Greece (including the Paleogene deposits of the Axios Basin, AXB) was compared with the Mesohellenic Trough (MHT) in NW Greece. Both basins are characterized by a thick sedimentary sequence of molassic-type strata (3-5 km thickness) of Tertiary age, overlain unconformably by Miocene-Pliocene and Quaternary deposits. Molassic sedimentation started almost simultaneously in both areas during the Mid-Late Eocene but it finished in different time, in the Mid-Late Miocene for the MHT and the Late Oligocene for the THB, respectively. Sedimentation in THB was also linked with an important calc-alkaline and locally shoshonitic, acid to andesitic magmatism of EoceneOligocene age. We interpreted the MHT as a polyhistory strike-slip and piggy-back basin, above the westwardemplacing Neotethyan ophiolites and Pelagonian units on the cold Hellenic accretionary prism. In contrast to the MHT, the studied portion of the THB evolved as a Paleogene supra-detachment basin above the strongly extended during the Eocene-Oligocene Rhodope metamorphic province. The syn-depositional magmatic products, linked possibly with subduction processes in Pindos or Axios ocean(s). In any case, MHT and THB are related to inferred oblique convergence of the Apulia plate and the internal Hellenic units.