Marine ecosystems and their inhabitants are increasingly under threat from climate change, competition with humans for resources, and pollution. Species that are endemic to particular currents or regions of the world's oceans have the potential to be at higher risk due to localized overfishing, pollution, or locally severe impacts of climate change such as more intense, or longer, El Niño Southern Oscillation events. Understanding patterns of population differentiation in endemic marine organisms may be particularly important for their conservation and persistence. Peruvian Boobies (Sula variegata) are endemic to the Humboldt Current upwelling system and have experienced population fluctuations throughout their evolutionary history due to both dramatic reduction of food supplies, and anthropogenic influence over the last ~150 years. Recent research on other members of the Sulidae indicates that populations of these primarily tropical seabirds show a high degree of genetic differentiation; however, the sister species of the Peruvian Booby, the Blue-footed Booby (S. nebouxii), exhibits only weak range-wide population genetic structure. We characterized population genetic differentiation and diversity in 153 Peruvian Boobies using sequence variation of 540 base pairs of the mitochondrial control region and seven microsatellite loci. Although we found evidence of panmixia, a signature of isolation by distance appears to exist between the five sampled colonies. We also found unexpectedly high genetic diversity given this species' recent population decline. Our results are similar to those for the Humboldt Penguin (Spheniscus humboldti), another endemic of the Humboldt Current upwelling system. © 2010 Dt. Ornithologen-Gesellschaft e.V.