The antiquity of the use of seaweed to feed domestic animals was investigated through carbon (δ13C) and oxygen (δ18O) isotope analysis of tooth enamel bioapatite. The analysis was performed on sheep and cattle teeth from two Neolithic sites in Orkney (Scotland). At the Knap of Howar, c. 3600 bc, carbon isotopes reflect grazing on terrestrial plants throughout the year for both sheep and cattle, with no contribution of seaweed to their diet. At the Holm of Papa Westray North (HPWN), c. 3000 bc, significant contribution of seaweed to the sheep diet during winter is indicated by bioapatite δ13C values as high as −5.7‰, far outside of the range of values expected for the feeding on terrestrial C3 plants, and δ18O values higher than expected during winter, possibly caused by ingestion of oceanic water with seaweed. Ingestion of seaweed by sheep at HPWN might have been necessitated by severe reduction of pastures during winter. Results suggest that sheep ingested fresh seaweed rather than dry fodder, perhaps directly on the shore as sheep do nowadays on North Ronaldsay. A significant difference between the two populations is the exclusive reliance on seaweed by the North Ronaldsay sheep, which have developed physiological adaptations to this diet. Contribution of seaweed to the sheep winter diet at HPWN might have been a first step towards this adaptation.