Previous studies identified the Amazon river dolphin (Inia geoffrensis) as the species frequently traded in public markets of Pará and Amazonas State (Brazil). In order to investigate the geographic origin and the taxonomic identification of these specimens we analysed 21 samples provided by residents of the city of Belém and vicinities (Pará State, Brazil), presumably purchased in the ‘Ver-o-Peso’ Market (Belém) or the Manaus Municipal Market. DNA was extracted from dehydrated genitalia or from genitalia conserved in alcohol and the cytochrome b gene was PCR-amplified. Phylogenetic analyses showed identical topologies in both MP and NJ trees, with Sotalia splitting into two groups, one clade comprising the estuarine dolphin (S. guianensis) and all eight haplotypes from market-samples and another one, comprising the tucuxi (S. fluviatilis) haplotypes from the GenBank. Our findings indicated that the marine species is under a stronger commercial pressure than the Amazonian river dolphin (I. geoffrensis) and the tucuxi (S. fluviatilis) in the region. Therefore population dynamic studies as well as population monitoring should be carried out in order to evaluate the effects of this commercial hunting on the species and its local populations. The marine dolphins have been incidentally captured in gill-nets in the region, suggesting that these activities must also be monitored at the same time that social programmes must be implemented in order to inform and clarify local community and people involved in fishery activity to avoid that more animals might be captured and killed.