An unexpectedly large number of well-preserved fossil ziphiid (beaked whale) skulls trawled from the seafloor off South Africa significantly increases our knowledge of this cetacean family. The eight new genera and ten new species more than double the known diversity of fossil beaked whales and represent more than one-third of this family (fossil and extant). A cladistic parsimony analysis based on 18 cranial characters suggested that some of these fossil taxa belong to the three extant ziphiid subfamilies, whereas others might represent extinct ziphiid lineages. Such high fossil ziphiid diversity might be linked to the upwelling system and the resulting high productivity of the Benguela Current, which has been in place and influenced conditions of the shallower waters along the southwest coast of South Africa and Namibia since the Middle Miocene. Both fossil and extant South African beaked whale faunas show a wide range in body size, which is probably related to different dietary niches and to wide exploration of the water column. Moreover, most South African fossil ziphiids share two morphological traits with extant species, which indicates that some of the behaviours associated with these traits had likely already developed during the Neogene: 1) the absence of functional maxillary teeth—providing clear evidence of suction feeding; and 2) the heavy ossification of the rostrum in specimens assumed to represent adult males—a feature which likely helps prevent injury and damage on impact during male–male fighting.