The Cenozoic East African Rift System (EARS) extends from the Red Sea to Mozambique. Here we use seismic reflection and bathymetric data to investigate the tectonic evolution of the offshore branch of the EARS. The data indicate multiple and time transgressive neotectonic deformations along ~800km of the continental margin of northern Mozambique. We observe a transition from a mature rift basin in the north to a juvenile fault zone in the south. The respective timing of deformation is derived from detailed seismic stratigraphy. In the north, a ~30km wide and more than 150km long, N-S striking symmetric graben initiated as half-graben in the late Miocene. Extension accelerated in the Pliocene, causing a continuous conjugate border fault and symmetric rift graben. Coevally, the rift started to propagate southward, which resulted in a present-day ~30km wide half-graben, approximately 200km farther south. Since the Pleistocene, the rift has continued to propagate another ~300km, where the incipient rift is reflected by subrecent small-scale normal faulting. Estimates of the overall brittle extension of the matured rift range between 5 and 12km, with an along-strike southward decrease of the extension rate. The offshore portion of the EARS evolves magma poor, similar to the onshore western branch. The structural evolution of the offshore EARS is suggested to be related to and controlled by differing inherited lithospheric fabrics. Preexisting fabrics may not only guide and focus extension but also control rift architecture.