The Gulf of Izmit is a critical basin in assessment of the kinematics of the North Anatolian Fault (NAF) at the eastern margin of the Sea of Marmara. The available seismic reflection data do not provide sufficient and clear evidences to outline the deeper structures because of limited penetration. In agreement with the known main tectonic elements from available seismic data and multi-beam bathymetry, new magnetic data gathered within the scope of this study show E-W trending anomalies and permit us to outline satisfactorily the deeper tectonic setting of the gulf region. The northern strand of the NAF can be evidently correlated with the maxima on the magnetic profiles, implying a significant thinning in the crust along the weakness zone placed between the Istanbul Zone and Karakaya Complex. Such a tectonic structure must have been formed as parallel transform strike-slip pressure, which is different from the characteristic negative-flower structure observed at the East Marmara trough. This pattern occurs in a relatively narrow zone, because it has been superimposed on a paleo-tectonic lineament.