Sexual segregation during foraging is common in birds and may occur at different temporal and spatial scales. In this study we explored the degree of sexual segregation in the Black Skimmer Rynchops niger by studying the species and sizes of prey consumed by either sex. Moreover we assessed the distribution of the sexes over the study area. We developed a multivariate tool for sex determination in Black Skimmers by using morphometric measurements from birds of known sex. Birds captured with mist nets and museum skins were analysed. The sex of birds was determined by PCR amplification of DNA or by gonad inspection. The fish prey remains obtained from spontaneous regurgitations of captured birds were used to estimate total length and weight of consumed fish prey. The bulk of the diet of both sexes was generally composed of the same species (mostly silversides Odontesthes spp.), but males consumed larger prey than females. The sex ratio in the lagoon was strongly skewed towards females. We discuss the implications of sexual segregation for habitat and species conservation measures.