Intracontinental elevated plateaus remain geomorphologic features which are poorly studied. Their genesis requires a coupling between climate and deformation. The Fish River canyon (southern Namibia), the second largest canyon of the Earth, carved the South-African plateau on 550 m along 65 km. This study reveals that the upper and the lower segments are shaped by NE-SW and north-south grabens, respectively. These deformations increased the meandering and the vertical incision mainly in the lower canyon. However the river main trend was not drastically modified attesting that the river was ancient and that the rate of the vertical displacement was slow compared to the erosion rate. The main incision occurred during a NW-SE stretching of Plio-Pleistocene. These stretching episodes belong to two deformation phases previously poorly described in the South-African plateau. These widespread stretching phases are interpreted as a result of deep mantle dynamics affecting the inner African continent. Keywords: Canyon, Namibia, Tectonics, Mantle.