Sharks of the genus Carcharhinus exhibit subtle morphological differences that are difficult to observe because of the common practice of head and fin removal, making species identification challenging. A total of 317 sharks, commonly called ‘cação-baia’ (large individuals) or ‘machote’ (small size) in Brazil, were captured by the tuna fleet at the Santos and Guarujá fishery ports on the southeastern coast of Brazil and identified at the species level by multiplex PCR. The Internal Transcribed Spacer 2 region of ribosomal DNA was amplified using universal primers, and species-specific primers were used for some of the Carcharhinus species. A total of 313 shark carcasses were directly identified by multiplex PCR. Four carcass samples did not amplify; therefore, the partial COI sequences were used to confirm their taxonomic identity. The results show that more than one species was being traded under the same commercial designation, including some Carcharhinus species that are under protection by federal legislation. Such species misidentification directly affects the long-term sustainability of sharks.