The Bay of Bengal is one of the most productive ecosystems in the northern Indian Ocean and it harbours a rich community of cetaceans, including Indo-Pacific bottlenose (Tursiops aduncus) and humpback (Sousa spp.) dolphins. The taxonomy of these genera has been controversial, but within the Indian Ocean both seem to be divided into phylogenetically discrete units that range from the east to the west. Within the Sousa genus, S. plumbea is distributed in the western Indian Ocean while S. chinensis is distributed in the eastern Indian and western Pacific Ocean. T. aduncus has a discontinuous distribution throughout the Indo-Pacific Ocean and two different phylogenetic units are known to exist, one along the eastern African coast and another one in the eastern Indian and west Pacific Ocean. In this study we investigate the phylogeography of Indo-Pacific humpback and bottlenose dolphins in the northern Bay of Bengal. We sequenced the mitochondrial DNA control region for 17 bottlenose and 15 humpback dolphins and compared the results with previously published sequences within each genus. In both cases, we found that Bangladesh dolphins are genetically different from neighbouring populations. While the Bangladesh T. aduncus seem to be more closely related to the African T. aduncus form than the Pacific form, Sousa spp. seem to be more closely related to individuals from Australia. The genetic uniqueness of these populations has important evolutionary implications, due to their isolation, coastal distribution in a geographic cul-de-sac characterized by an extreme infusion, redistribution and recycling of biological productivity, and conservation implications since their survival is threatened in particular by fatal interactions with fisheries. We suggest that the particular and extreme oceanographic conditions found in the Bay of Bengal may be driving speciation in these dolphins and other marine megafauna.