Numerous studies have addressed various aspects of the East African Rift system but surprisingly few on the offshore continuation of the south-eastern branch of the rift into the Mozambique Channel. The most prominent article has been published almost 30 years ago by Mougenot et al. (1986) and is based on vintage seismic data. Several studies investigating earthquakes and plate motions from GPS measurements reveal recent deformation along the offshore branch of the East African Rift system. Slip vectors from earthquakes data in Mozambique’s offshore basins show a consistent NE direction. Fault plane solutions reveal ~ E-W extensional failure with focal depth clustering around 19 km and 40 km, respectively. Here, we present new evidence for neotectonic deformation derived from modern seismic reflection data and supported by additional geophysical data. The modern rift system obviously reactivates structures from the disintegration of eastern Gondwana. During the Jurassic/Cretaceous opening of the Somali and Mozambique Basins, Madagascar moved southwards along a major shear zone, to its present position. Since the Miocene, parts of the shear zone became reactivated and structurally overprinted by the East African rift system. The Kerimbas Graben offshore northern Mozambique is the most prominent manifestation of recent extensional deformation. Bathymetry data shows that it deepens northwards, with approximately 700 m downthrown on the eastern shoulder. The graben can be subdivided into four subbasins by crosscutting structural lineaments with a NW-SE trend. Together with the N-S striking graben-bounding faults, this resembles a conjugate fault system. In seismic reflection data normal faulting is distinct not only at the earthquake epicenters. The faults cut through the sedimentary successions and typically reach the seafloor, indicating ongoing recent deformation.