In the shallow coastal waters of the Danish archipelago, eelgrass (Zostera marina) forms extensive and extremely productive stands, which support food webs that are isotopically distinct from those based on the primary productivity of marine phytoplankton. The isotopic signatures of eelgrass and phytoplankton food webs explain much of the variation in δ13C, δ15N and δ34S values in marine vertebrate remains recovered from prehistoric coastal sites in Denmark. Isotope data from human and dog remains reflect the overwhelming importance of the eelgrass biotope to the fisher-hunter-gatherer subsistence during the Late Mesolithic Ertebølle epoch (∼7400-5800 cal BP). By recognising eelgrass and pelagic resources as isotopically distinct, we obtain more accurate diet reconstructions and dietary 14C reservoir effect corrections for Ertebølle individuals. Longstanding research issues, including technology, palaeodemography, and the resilience and sustainability of the Ertebølle economy need to be reassessed in view of the isotopic signature and productivity of the eelgrass biotope in Danish waters. Eelgrass productivity is also pertinent to comparisons between Ertebølle and Neolithic economies in Denmark, and between fisher-hunter-gatherer adaptations in Denmark and neighbouring regions, and may be key to understanding the much-discussed delay in the transition to farming.