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As a result of phenotypic plasticity, the cupped oysters (Crassostrea) are difficult to identify by means of their morphology. However, molecular DNA markers are a useful means of discriminating among these species. Cupped oysters are one of the most widely cultured marine invertebrates and correct species identification is important in aquaculture. Moreover, the molecular phylogeny of the genus Crassostrea and the subfamily Crassostreinae is still not clear. In order to identify the Brazilian cupped oysters and to clarify the phylogenetic relationships of these species, we sequenced a fragment of mitochondrial DNA (16S rRNA gene) from 120 specimens collected at nine different sites distributed along the Brazilian coast. The results identified two native species of oyster: Crassostrea gasar, from the Amazon to the Parnaíba delta; and Crassostrea rhizophorae, from the northeast (Fortim) to the south of Brazil. An exotic Crassostrea species, closely related to Indo-Pacific Crassostrea, was found in one location in the north of Brazil. Crassostrea showed monophyly and the Atlantic oysters are clearly separated from the Indo-Pacific cluster. [ABSTRACT FROM AUTHOR]