Rynchops niger intercedens, one of the South American subspecies of the Black Skimmer, is a widely distributed neotropical bird for which many ecological aspects, such as migratory routes and site fidelity, are unknown. Two distinct breeding phenologies have been reported for this subspecies, which may create the genetic isolation of populations. Six microsatellite loci were used to study the genetic structure of the Black Skimmer in southern South America, comparing breeding populations from Brazil and Argentina and individuals from the main nonbreeding site at Argentina. A weak genetic differentiation between colonies, although statistically significant, was observed. This low genetic structure (despite different breeding phenologies) could be explained by demographic history of these populations and/or the effect of a very important non-breeding site in southern South America shared by these populations. Further studies applying a broader range of molecular markers plus improvement of extant banding efforts are required to better understand the dispersal mechanisms of this species.