The Portuguese oyster, Crassostrea angulata, was introduced from Portugal to the French Atlantic Coast in the 1860s. C. angulata quickly settled and expanded and leaded to the development of a new aquacultural industry in France. In the late 1960s, mortality associated with the detection of an iridovirus, led to the wipe out of C. angulata from French Atlantic waters and to the massive introduction of C. gigas to sustain production. In Southern Europe, similar symptoms were also observed in natural stocks of C. angulata from Sado River (Portugal) and from the area of Cadiz (Spain). Nowadays, only very few «pure» populations of C. angulata remain in southern Europe. These populations are potentially endangered by the current expansion of C. gigas aquaculture, as well as the pollution of their habitats. In October 2002, cupped oysters from Sado and Mira estuaries (Portugal) were sampled and analysed using a mitochondrial DNA marker previously shown to be diagnostic for C. angulata and C. gigas. All oysters analyzed revealed haplotypes characteristic of C. angulata. We also analyzed wild cupped oysters from Ria Formosa (Southern Portugal), an area where C. gigas is known to be farmed. These samples were analysed with a «pseudospecific» nuclear DNA marker previously developed to differentiate populations of C. angulata and C. gigas. In addition, a new mitochondrial marker was developed that also allows the identification of other oyster species that exist in the area, namely the European oyster Ostrea edulis and the rock oyster Ostreola stentina. Despite the sympatric occurrence of C. angulata and C. gigas in Ria Formosa our results suggest that there is minimal hybridization between the two taxa. Furthermore, despite very limited natural beds, C. angulata seems to recrute much more than farmed C. gigas, indicating a differential ability to settle of these two taxa in Ria Formosa.