We update the systematics and comparative anatomy of the genus Hispanomeryx Morales, Moyà-Solà and Soria, 1981 through the description of a new and abundant fossil material from the middle Miocene localities of Toril-3, Manchones-1 and Manchones-2, Zaragoza Province, Spain. Hispanomeryx was only known by dental remains, mainly mandibles and lower teeth, and very scarce postcranial material; the fossil sample studied here includes cranial, mandibular, dental and postcranial remains, and it allows us to describe in depth, for the first time, the anatomy of the genus. We also erect the new species Hispanomeryx daamsi. The material is good and abundant enough as to include Hispanomeryx in a cladistic analysis performed to explore its phylogenetic relationships within the Pecora. This analysis includes Hispanomeryx in a monophyletic Moschidae (musk deer) composed by Micromeryx, Hispanomeryx, ‘Moschus’ grandeavus and extant Moschus, and recovers a clade composed by moschids and bovids; this is the first time that a Moschidae-Bovidae sister-group relationship is backed-up by morphological data. A direct sister-group relationship between Hispanomeryx and the Bovidae is thus rejected. Several taxa previously assigned to the ‘Moschidae’ are rejected as true moschids. Finally, the cladistic phylogenetic analysis of Hispanomeryx demonstrates its monophyly and shows a basal species, H. aragonensis Azanza, 1986, and a clade formed by H. duriensis Morales et al., 1981 and H. daamsi sp. nov, characterized by the presence of more derived lower molars than those of H. aragonensis.