Neogene basins/grabens along with exhumed core complexes make up the fundamental components of western Anatolia within the geologic framework of the Aegean Extensional Province. The Neogene basins are divided into two based on their orientation and contrasting lithostratigraphic packages: (1) the NE–SW basins that are dominated by materials either derived from the Menderes Massif and/or İzmir-Ankara-Erzincan suture zone-related units during the Lower Miocene and sedimentation that had mostly ended by the end of the latest Miocene, (2) E–W trending basins that are known to be devoid of Tethyan ophiolitic material and contain Miocene and Plio-Quaternary deposits. The relationship between the two sets of basins has been unclear, with some suggesting that E–W trending grabens are younger than the NE–SW trending grabens. Here, we reported results from the deep (up to 3840 m) geothermal wells from the Alaşehir sub-basin of the E–W trending Gediz Graben. Our analysis reveals that the Neogene graben fill is thicker than previously documented and contains ophiolite-derived clastics at its base. We proposed that the Alaşehir sub-basin has a similar early Miocene configuration as the Uşak-Güre basin and the Gediz Graben represents an inherited structure of the NE–SW trending grabens.