We investigated the crustal structure beneath the Marmara region and the surrounding area in the western part of the North Anatolian fault zone. These areas have high seismicity and are of critical significance to earthquake hazards. The study was based on travel-time tomography using local moderate and micro-earthquakes occurring in the study area recorded by the Multi-Disciplinary Earthquake Research in High Risk Regions of Turkey project and Kandilli Observatory and Earthquake Research Institute. We selected 2131 earthquakes and a total of 92,858 arrival times, consisting of 50,044 P-wave and 42,814 S-wave arrival times. We present detailed crustal structure down to 50 km depth beneath the Marmara region for P- and S-wave velocities using the LOTOS code based on iterative inversion. We used the distributions of the resulting seismic parameters (Vp, Vs) to pick out significant geodynamical features. The high-velocity anomalies correlate well with fracturing segments of the North Anatolian fault. High seismicity is mostly concentrated in these segments. In particular, low velocities were observed beneath the central Marmara Sea at 5 km depth.