The study of more than 500 single- and multi- channel seismic records enabled the generation of a detailed palaeo-bathymetric map of the Messinian surface over most of the Alboran Basin, Western Mediterranean. This regional surface is characterized by several erosional features (channels, terraces and canyons) and topographic highs (structural, volcanic and diapiric in origin). The most prominent feature is the incised Zanclean Channel crossing the entire basin, its entrenchment having been associated with the opening of the Strait of Gibraltar and subsequent inflow of Atlantic waters. The incision depth of the channel is variable, suggesting local variations in the erosive capacity of the Atlantic inflow, conditioned mainly by the regional basin topography and the local presence of topographic highs. Adjacent to this channel along the Spanish and Moroccan margins, and near the Strait of Gibraltar, several submarine terraces developed at different depths suggest a pulsed flooding of the Alboran Basin. There could have been two major inflow phases of Atlantic water, one shortly before and another during the Zanclean flooding, the latter accompanied by periods of relative sea-level stillstands that enabled terrace development. Alternatively, these features were all generated during the main flooding evident and subsequent pulsed infilling of the basin.