The European flat oyster, Ostrea edulis, is an emblematic and ecologically important species that was fished to virtual extinction in Belgian and Dutch waters in the 19th century. We report on recent findings of live specimens in Belgian and Dutch waters, an indication for the presence of O. edulis in these waters. Though small, these relict populations provide possibilities for natural recovery of O. edulis reefs in Belgian and Dutch waters, provided the oyster’s habitat requirements are restored (e.g., exclusion of bottom disturbance). We suggest investigating whether a natural, yet slow, recovery using fisheries closures and gravel bed restoration is a feasible alternative to the currently envisaged human-mediated re-introduction of O. edulis in the North Sea. We identify and address the challenge of O. edulis detection and identification as an important issue blurring the true presence and distribution of oysters.