Earth’s deep oceans remains less well understood than the surface of Mars. Beaked whales (ziphiids) are among the most visible inhabitants of the abyss, due to their large size and worldwide distribution, yet their diversity and ecology remain obscure. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari’s beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous people of the lands from which the species holotype and paratypes were recovered. Mitogenome and ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. eueu and North Atlantic True’s beaked whale (M. mirus), with which it was subsumed. Revised morphometric analyses of skulls separate the species. A time-calibrated mitogenome phylogeny and analysis of two nuclear genomes indicate divergence began ca 2 million years ago (Ma), with geneflow ceasing 0.35-0.55 Ma. This is an example of how deep-sea biodiversity can be unravelled through increasing international collaboration and genome sequencing of archival specimens. Our consultation and involvement with Indigenous groups offers a model for broadening the cultural scope of the scientific naming process.

See article supplementary materials for methods and sample IDs.