Abstract This paper presents selections from and a synthesis of a high resolution bathymetric, sparker and deep-towed seismic reflection data set recently acquired by the French Ifremer R.V. Le Suroı̂t in an E–W deep trough that forms the northern half of the Sea of Marmara in NW Turkey. It includes the first high resolution complete bathymetric map of this area. A single, throughgoing dextral strike–slip fault system, which is the western continuation of the northern branch of the North Anatolian Fault, cuts this trough lengthwise and joins the 1999.8.17 Kocaeli earthquake fault with the 1912.8.09 Şarköy–Mürefte earthquake fault, both of which display strike–slip offset. In its eastern one fourth, the structure follows closely the northern margin of the deep trough, whereas in the west it hugs its southern margin. The eastern one fourth of the structure has a minor component of its displacement distributed across the deep trough owing to a possible original bend in the course of the dextral structure. The present course of the North Anatolian Fault in the Sea of Marmara originated some 2×10 5 a ago, by cutting across the older basin fabric generated by a dominant NNE–SSW extension before it began taking up major motion in the Pliocene.