The copper or bronze whaler shark (Carcharhinus brachyurus) is a large, coastal top predator that is vulnerable to overexploitation. We test the null hypothesis that copper sharks are panmictic throughout the southern hemisphere. We analysed part of the mitochondrial control region (mtCR) in 120 individuals from eight sampling areas, defining 20 mtCR haplotypes (h = 0.76 ± 0.06, π = 0.016 ± 0.0007). Significant genetic structure was detected among the following three major coastal regions separated by oceanic habitat: Australia-New Zealand, South Africa-Namibia and Per (AMOVA Φ ST=0. 95, P < 0.000001). A major phylogeographic discontinuity exists across the Indian Ocean, indicating an absence of at least female-mediated gene flow for ∼3 million years. We propose that this species originated in the Atlantic, experienced vicariant isolation of Pacific and Atlantic lineages by the rise of the Isthmus of Panama and, subsequently, dispersed across the Pacific to colonise Australasia. Oceanic expanses appear to be traversed over evolutionary but not ecological timescales, which means that regional copper-shark populations should be assessed and managed independently.