Despite the economic importance of oysters due to the high aquaculture production of several species, the current knowledge of oyster phylogeny and systematics is still fragmentary. In Europe, Ostrea edulis, the European flat oyster, and Ostreola stentina, the Provence oyster or dwarf oyster, are both present along the European and African, Atlantic and Mediterranean, coasts. In order to document the relationship not only between O. stentina and O. edulis, but also with the other Ostrea and Ostreola species, we performed a sequence analysis of the 16S mitochondrial fragment (16S rDNA: the large subunit rRNA-coding gene) and the COI fragment (COI: cytochrome oxidase subunit I). Oysters were sampled from populations in Portugal (two populations), Tunisia (two populations) and Morocco (one population), identified as O. stentina on the basis of shell morphological characters. Our data supported a high degree of differentiation between O. stentina and O. edulis and a close relationship between O. stentina and both Ostrea aupouria (from New Zealand) and Ostreola equestris (from Mexico Gulf/Atlantic). The status of this geographic disjunction between these closely related species is discussed. Furthermore, although identified in a separate genus Ostreola by Harry (Veliger 28:121-158, 1985), our molecular data on O. stentina, together with those available for the other two putative congeneric species, O. equestris and Ostreola conchaphila, would favour incorporation of Ostreola in Ostrea. Finally, a PCR-RFLP approach allowed the rapid identification of O. edulis and O. stentina.