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