The flat oyster Ostrea edulis is the species endemic to European coasts, both Atlantic and Mediterranean. It has been exploited since Roman times, but its aquaculture production decreased from around 20000 tons in the 1950's to 1500 tons today because of two successive diseases due to the intracellular parasites Marteilia refringens and Bonamia ostreae. Since 1985, Ifremer has been undertaking a breeding program to produce families of oysters tolerant to Bonamia. In this context, a further step would be to identify QTLs for resistance to this parasite. Therefore, as a first step a genetic map is now being built. The establishment of a genetic linkage map will provide a foundation for the mapping of QTLs, with the ultimate objective to implement marker-assisted selection in O. edulis.