Abstract We analyze 2200 km of multi-channel seismic reflection profiles that have become recently available in the Sea of Marmara. This analysis benefits from the recent acquisition of multi-beam bathymetric data covering the axial portion of the northern basins. We conclude that the northern Sea of Marmara is at present cut by an active continuous strike–slip fault system, that we call the Marmara Fault. It links the 270° İzmit portion of the northern branch of the North Anatolian Fault to the east of the sea to the 245° Ganos Fault to the west. The Marmara Fault itself consists of two main parts. The western one is a single 80 km long fault. It follows a 265° direction that differs by 20° from the direction of the Ganos Fault. At its northeastern extremity, it turns toward the northern margin of the Çınarcık Basin. This western part of the fault is seismically quite active. The eastern part is more complex. It extends over 65 km in a 280° direction. There is thus a 10° clockwise rotation with respect to the 270° İzmit Fault strand that should result in a slight extensional component. Within the eastern Çınarcık Basin, this part of the Marmara Fault has two parallel branches, 10 km apart, the northern one near the foot of the northern slope, the southern one near the foot of the southern slope. A shortening zone occupies the northwestern corner of the Çınarcık Basin and much of the adjacent eastern Central High and separates the northern branch from the western one. The southern branch on the other hand may cross the eastern Central High along a narrow 280° valley. The data we have provide no definitive evidence on which of these two branches carries most of the motion. The establishment of the present trace of the fault through the Marmara Basin is contemporaneous with a recent phase of deposition of deep giant ripples, parallel to the bathymetric slope contours and adjacent to the turbidites basin deposits. The base of these deep basins sedimentary deposits is marked by a widespread erosional unconformity below which lies a gently folded sedimentary sequence that may consist of shallow Thrace Basin deposits.