Seismic reflection and multibeam echosounder data were acquired in the Mozambique Channel in 2014 and 2015 during the PTOLEMEE, PAMELA-MOZ02 and -MOZ04 marine surveys aboard the RV Atalante and Pourquoi Pas? These data revealed that an active fault system is deforming the oceanic lithosphere of the Mozambique Basin which has developed during Jurassic-Cretaceous times. The correlation between the fault system and the arrangement of earthquake epicenters suggests that this tectonically active zone directly connects northward with the southern part of the eastern branch of the East African Rift System which corresponds to the seismically active graben system bounding the northern part of the Davie ridge. The fault zone extends southwestward of the Mozambique Ridge along the same trend as the Agulhas-Falkland transform fault zone. The general organization of the fault zone shows the characteristics of an extensional system north of the Mozambique Channel (north of the Europa Island) and a right-lateral transtensional system with coeval normal faults and strike-slip faults south-west of Europa. This tectonic activity is associated with volcanic activity since at least Late Miocene times. Our findings emphasize that the eastern branch of East African Rift System is extending largely toward the south, not only in continental domains but also through the oceanic lithosphere of the Mozambique basin. This fault zone is participating to the complex plate boundary between the main African continent (Nubia Plate) and Madagascar (Somalia Plate).