Archaeological fieldwork at Hjarnø Sund in Horsens Fjord (eastern Jutland, Denmark) has explored an eroding Mesolithic shell midden. Its stratigraphy is characterized by two layers, containing marine mollusk taxa typically collected by Mesolithic hunter-gatherers for food. In the field, the lower layer appeared to be dominated by oysters (Ostrea edulis), while the upper one by cockles (Cerastoderma edule), which was confirmed by our zooarchaeological study. Accelerator mass spectrometry radiocarbon (AMS 14C) dating on shells and paired charcoal samples from the two layers indicate that these are chronologically consecutive (separated by as little as 0–163 yr [95.4%]) and that the oyster-to-cockle shift dated between ~5500–5300 and ~5300–5200 cal BC (around or just after the Kongemose/Ertebølle transition). The shell midden at Hjarnø Sund is, thus, one of the oldest-known in Denmark, demonstrating that intensive shellfish exploitation was a hallmark of the Ertebølle culture from its inception. Oyster-to-cockle shifts, thus, also occurred at times other than the Mesolithic–Neolithic Transition and may have been ultimately caused by local shoreline displacements, resulting from changes in sedimentation, possibly induced by drops in relative sea level.