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Anthropogenic pressures on the marine environment have escalated and shellfish habitats have declined around the world. Recently, Marine Protected Areas (MPAs) have rapidly increased in number and extent, but in Europe as elsewhere, management baselines rarely account for historical conditions.In the present study, the Dornoch Firth protected area (NE Scotland) was investigated as well as three adjacent inlets and 50 km of open coastline. The area has low levels of industrial development, is sparsely populated and conservation features were previously considered “Favourable”. The aim of the present study was to investigate the historical presence of native oyster (Ostrea edulis) beds, a habitat that is now rare and of conservation importance throughout Atlantic Europe.Centred on the protected area, but also gathering broader information from East Scotland, an interdisciplinary review was made of archaeological records, navigational charts, historical maps, museum collections, land-use records, fisheries records, public online databases and naturalists’ records. Intertidal and subtidal surveys were also conducted and sample oyster shells were radiocarbon dated.The present study shows that O. edulis occurred in the inlets and open coast areas of NE Scotland, and specifically in the protected area: Probably since the end of the last glaciation to the late 1800s when they were likely fished to extinction. Habitat restoration in protected areas is an emerging global theme. However, marine habitat restoration is highly unusual and European oyster restoration is presently confined to remnant populations with a clear history of exploitation or dwindling associated fisheries. An interdisciplinary review of baselines will probably show scope for O. edulis restoration in many other European MPAs.