This study brings new insights to elucidate the three dimensional (3-D) seismic velocity structure of the Aegean region of Turkey by using Local Earthquake Tomography (LET). The study area has remarkable potential for geothermal resources. To provide the subsurface geological structure of seismogenic layers and geothermal areas, we develop new high-resolution depth-cross sections through Buyuk Menderes, Kucuk Menderes and Gediz grabens. Travel times of almost 265.000 readings (14.963 P-phase and 11.969 S-phase picks) from 2.085 well-located events recorded between 2007 and 2016 by a permanent seismic network of 75 broad-band seismometers were used to precisely interpret the 3-D Vp (lithological) and Vp/Vs (petrological) models of the study area. We detected four main layers down to 35-40 km depths with different Vp velocities ranging from 3.5 to 8.5 km/s. Mid-crustal interface (Conrad discontinuity) is discovered at 15 km depth in nearly all depth-cross-sections. Our results suggest an average of 25 km Moho depth in the Aegean region of Turkey. The depths range from around 18 km beneath SE of Aydin to 29 km beneath Aliaga, and approximate values of 19, 25 and 31 km beneath the Doganbey, Kutahya and Selendi-Demirci regions, respectively. The geothermal areas of the studied region are imaged by Vp and Vp/Vs anomalies. We propose the Aliaga, Denizli, Doganbey and Kosk areas as low Vp, low Vp/Vs anomalies which are an indicator of steam, CO2 or a mixture of both. Low Vp, high Vp/Vs models, suggesting geothermal fluids, are clearly visible near the Buharkent, Gumuskol, Guzelhisar, Kosk, Kuyucak, Saraykoy and Suzbeyli regions. We also report that the Bademler, Candarli, Kalekoy, Karahalli, Merdivenli, Ortakoy, Saruhanli, Yelki and Yuntdagikoseler regions might be good candidates for new potential geothermal resources.