On the basis of a partial odontocete (toothed whale) skeleton (complete skull with associated ear bones, mandible, teeth, hyoid bones, and cervical vertebrae) from the middle Miocene (ca. 14–12 Ma) levels of the Pisco Formation at Cerro los Quesos, Pisco-Ica desert, southern coast of Peru, a new genus and species of beaked whale (Ziphiidae), Nazcacetus urbinai, is described. This small ziphiid, the best documented fossil species to date, is characterized by a strong reduction of the upper and lower dentitions except for a pair of large apical mandibular teeth, a Tasmacetus-like vertex, a short mandibular symphysis, and the abrupt elevation of the dorsal margin of the mandible towards the coronoid process. A phylogenetic analysis indicates that Nazcacetus is a crown ziphiid, in a more crownward position than Berardiinae and Tasmacetus, but branching before the Hyperoodontinae and Ziphiinae lineages. Several morphological traits observed in Nazcacetus, including the reduction of teeth, the small temporal fossa, and the large hamular process, suggest that this taxon possessed the suction feeding capacities of Recent ziphiids, a specialization possibly related to the exploitation by the early ziphiids of a new ecological niche. The presence of large apical teeth on the mandible of Nazcacetus, a character highly dimorphic in recent ziphiids, might indicate that sexual dimorphism was already present as early in ziphiid evolutionary history as the middle Miocene, a hypothesis supported by the nested position of Nazcacetus in the ziphiid phylogenetic tree.