Ecological and community differences have been noted across coral reef ecosystems with varying levels of anthropogenic intrusion, with striking declines of apex predator densities documented where human presence has historically been the highest. Within western Atlantic waters, one of the most common predators inhabiting coral reef ecosystems is the Caribbean reef shark (Carcharhinus perezi). Given the vulnerability of this species to fisheries and its potentially important ecological role as an apex predator, we assessed the overall genetic diversity and connectivity across its tropical western Atlantic distribution using both nuclear and mitochondrial DNA. Caribbean reef sharks demonstrated extremely low levels of genetic diversity across all surveyed loci relative to all other shark species analyzed to date, which may be due to a recent evolutionary origin. Nevertheless, nuclear microsatellite loci revealed population structure between Brazilian sites and populations from The Bahamas and Caribbean Sea (FST > 0.0182; P 0.05). In contrast, concatenated mitochondrial and mitochondrial/nuclear sequences revealed low but significant genetic differentiation across most of the surveyed locations. These patterns may reflect either historical patterns of dispersal or contrasting patterns of movement between male and female sharks. Although tagging and tracking data suggest these animals typically exhibit strong site attachment, our study reveals complex population structure with evidence supporting contemporary long distance mixing, at least by males, which should be incorporated into management plans for this species.