Abstract The taxonomy of the South American river dolphins of the genus Inia has been a focus of intense debate. While traditionally it is thought to be composed of a single species with three geographically structured subspecies (Inia geoffrensis geoffrensis, I. g. humboldtiana, and I. g. boliviensis), recent molecular studies have highlighted substantial differentiation, suggesting the existence of two species (I. geoffrensis and I. araguaiaensis). Despite this evidence, the recognition of the specific status of these taxa has been hindered by inconsistent morphological diagnoses. Here, we aim to provide evidence for the morphological differentiation (or lack thereof) between subspecies and putative species. We employ geometrics and traditional morphometrics to measure skull variation to support efforts of integrative taxonomy. Our results show that morphometric diversity within the group is inconsistent with a single taxon. Morphometric evidence supports the traditional differentiation of three distinct morphotypes within the analyzed sample. These morphotypes largely correspond to described subspecies I. g. geoffrensis, I. g. humboldtiana—the latter differing from the former by size—and I. g. boliviensis, which differs from the remaining groups by shape. Furthermore, morphometric data show no differences between I. g. geoffrensis and a newly proposed species, I. araguaiaensis. Given the conservation importance of this genus and the different threats they are subject to, we strongly suggest an urgent integrative taxonomic treatment of the group to better protect these singular cetaceans.