Local adaptation and adaptive radiations are typically associated with phenotypic variation suited to alternative environments. In the marine environment, the nature of relevant ecological or environmental transitions is poorly understood, especially for highly mobile species. Here we compare three genetic lineages in the genus Tursiops (bottlenose dolphins), using linear measurements and geometric morphometric techniques, in the context of environmental variation in the northwest Indian Ocean. Cranial morphology was clearly differentiated comparing Tursiops truncatus and Tursiops aduncus, while a recently discovered genetic lineage, found in the Arabian Sea, was morphologically most similar to T. aduncus from the same region, but distinct for various measures, particularly metrics associated with the lateral dimension of the skull. The extent of divergence between T. truncatus and T. aduncus compared to differences between the T. aduncus lineages is consistent with the recent phylogeny for these species. Therefore, with the corroboration of genetic and morphological inference, we propose two conservation units of T. aduncus be recognized in the region at a sub-specific level so that their conservation can be managed effectively. We consider possible evolutionary mechanisms associated with regional habitat characteristics and the exploitation of distinct prey resources.