The taxonomic status of the Portuguese oyster Crassostrea angulata and the Pacific oyster Crassostrea gigas has often been a matter of controversy. Based on larval shell morphology, experimental hybridisation and electrophoretic studies of enzyme polymorphism several authors have considered these two species as being synonymous. During the recent years, several genetic studies based on mitochondrial DNA and microsatellites data have provided evidences that the two taxa are genetically distinct although closely related. Furthermore, karyotype analyses have also highlighted the close genetic similarity of these taxa in comparison with other cupped oyster species. However, a comparative analysis of restriction enzymes ideograms revealed differences between all chromosomes of C. angulata and C. gigas with the exception of chromosome 10. In addition, significant phenotypic differences between the two taxa were observed in terms of aquaculture production and eco-physiological characteristics. Different hypotheses were proposed to explain the separated geographic distribution of these close related taxa, C. angulata being present in Europe and C. gigas in Asia. Phylogenetic analyses firmly place both Portuguese and Pacific oysters within an Asian Crassostrea clade supporting the hypothesis of the introduction of C. angulata from Asia to Europe. Pure populations of C. angulata were observed in Taiwan as well as presumed mixed populations of C. angulata and C. gigas in Northern China. Remarkably, using equivalent amount of research on both taxa, the level of genetic variability of C. gigas (samples collected in different parts of the world) appears to be lower than that of C. angulata (samples collected in Portugal) based on cytochrome oxidase C sub-unit I haplotypes. This difference could be related to the dissemination of C. gigas from Miyagi Prefecture to different regions in Japan and other places in the world where the Pacific oyster was introduced.