The diet of the Little Tern (Sternula albifrons), an estuarine seabird species breeding in southern Portugal, was determined by separately identifying fish otoliths and scales found in pellets. Using both fish otoliths and scales showed that the diet of Little Terns was mainly composed of sand-smelts (Atherina spp.), but there were differences in secondary prey items. Species such as sardine (Sardina pilchardus), with very small and easily degraded otoliths, showed a higher percentage of occurrence in the diet using scale analysis. This study suggests that both methods should be used together to evaluate the diet of small estuarine seabird species.