The Levant continental margin is divided into two major segments by the Carmel structure, which extends from the Dead Sea fault into the eastern Mediterranean. New seismic reflection data over the unexplored northern segment are used for completing the structural framework of the Levant area, together with existing data south of it. Inclusive depth structural maps of the area were produced for the base Pliocene and base Messinian evaporites. Previous studies indicate that differences between the two segments are well expressed in the deep crustal structure. The present study, which focuses mainly on the shallow section, shows that these differences are maintained throughout the accumulation of young sedimentary units, and even in the bathymetry. This preservation of segmentation, both in the shallow and in the deep structure, insinuates that the two segments were formed through different continental breakup processes, which continue to dictate the style of sediment accumulation.