AbstractKnowledge of the diet of marine predators such as seabirds is fundamental to understanding the ecological cascades they may influence and the impact that environmental changes may have on them. Diet analysis of seabirds frequently relies on the identification of fish otoliths in pellets. However, it is recognised that the true dietary importance of fish with small and fragile otoliths is likely underestimated, requiring an additional method. In this study, we compared the identification of otoliths with that of vertebrae in pellets to gain a more complete picture of seabird diet. We identified fish otoliths and vertebrae from 2584 great skua Stercorarius skua pellets collected between 2014 and 2017 from five colonies in Scotland. Diet varied markedly between colonies, comprising mostly fish in Shetland and mostly birds in St Kilda. 10% of pellets contained otoliths compared to 70% with fish vertebrae. Atlantic herring Clupea harengus and Atlantic mackerel Scomber scombrus were the most common fish species at all colonies when using vertebrae in contrast to being virtually absent when using otoliths. Conversely, the occurrence of Norway pout Trisopterus esmarkii and pollock Pollachius pollachius otoliths was six and eight times, respectively, higher than for vertebrae. Therefore, combining data from both otoliths and vertebrae provides a more complete profile of the fish component of seabird diet. This is fundamental to improving our understanding of the impacts of marine management policies on seabirds, as well as how changes in the population size of such seabird species might affect their prey species.