Ziphiidae (beaked whales) are a successful family of medium- to large-sized toothed whales. Their extant members perform regular deep dives beyond the photic zone to forage for cephalopods and fish. Conversely, extinct long-snouted stem ziphiids are interpreted as epipelagic predators. However, some aspects of this hypothesis remain unclear due to the lack of clear morphological proxies for recognizing regular deep divers. We compared the forelimb, neck, and pterygoid sinus system of the fossil ziphiid Messapicetus gregarius with those of other odontocetes to evaluate the potential of these body regions as proxies to assess deep-diving specialization. The reconstructed musculature of the neck and forelimb of M. gregarius was also compared with that of other odontocetes. We also quantified variation in the proportions of the forelimb and the hamular fossa of the pterygoid sinus (HF) using 16 linear measurements. The degree of association between diving behaviour in extant odontocetes and these measurements was evaluated with and without phylogenetic correction. Reconstruction of the neck musculature suggests that M. gregarius possessed a neck more flexible than most extant ziphiids due to the lower degree of fusion of the cervical vertebrae and the large insertions for the M. longus colli and Mm. intertransversarii ventrales cervicis. While neck rigidity might be related to deep diving, differences in neck flexibility among extant ziphiids indicate a more complex functional interpretation. The relationship between forelimb morphology and diving behaviour was not significant, both with and without phylogenetic correction, suggesting that it cannot be used to assess deep-diving abilities with the parameters considered here. Measurements of the HF revealed successful to evaluate deep-diving abilities in odontocetes, with an enlargement of this structure in deep divers. Considering other evidence that suggests an epipelagic behaviour, we propose different scenarios to explain the observation of an enlarged HF in M. gregarius: (1) this species may have fed at different depths; (2) it performed deep dives to avoid potential predators; or (3) the enlarged HF and deep-diving habitat correspond to an ancestral condition, with M. gregarius returning to a more epipelagic habitat.