Sexual dimorphism is the phenotypic difference between males and females of the same species, characterized by different body size and plumage. Black Skimmers (Rynchops niger, n = 44 adults, n = 14 juveniles) were captured between December 2010 and April 2012 with mist nets during the non-breeding period in the Lagoa do Peixe estuary, southern Brazil. Black Skimmers showed conspicuous sexual size dimorphism, with males being significantly larger than females. Males were 29% heavier than females and significantly larger in six measurements (% sexual size dimorphism = 7–26%). We developed two discriminant functions, both correctly identifying the sex of > 97.7% of the individuals tested and found that head bill length alone was sufficient to predict the adult sex. The preferred habitat of Black Skimmers in this area was the barra region of the Lagoa do Peixe, where they can take advantage of the abundance of fish in the shallow water. Active molt was recorded in 62.5% of captured Black Skimmers. The molt scores of the primaries and the capture date showed a positive correlation, with lower scores observed in November/December and the highest scores in March/April. We found the intensity of red coloration of the culmen was not a good method for Black Skimmer sex determination in the field compared to molecular sexing, misclassifying 31.0% of individuals overall.