The Pacific oyster, Crassostrea gigas, has been voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry following a severe disease outbreak. Since then, the two species are in contact in southern Europe and therefore have the potential to exchange genes in a new environment. Whether C. gigas and C. angulata truly represent biological species, semi-isolated species of populations of the same species has been largely discussed. This has been recently clarified by a genome-wide approach providing empirical evidence for highly heterogeneous divergence patterns across the genome, attributed to reduced introgression in low-recombining regions since secondary contact. Up to now only one mitochondrial and one nuclear marker have been used to differentiate C. gigas and C. angulata. Here, we selected a subset of ancestry informative makers from existing genomic resources in order to (1) easily differentiate C. gigas and C. angulata, and (2) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic coasts. In this context several datasets were produced using 15 to 80 SNP markers.