The blue shark Prionace glauca is a cosmopolitan species that inhabits all oceans worldwide except the poles. Several IUCN regional assessments have classified   it as Near Threatened, mostly due to overfishing. Previous genetic studies that have used classical genetic markers failed to reject the hypothesis that the species is a single worldwide population (panmixia). As such, the blue shark was proposed to be an archetype of the ‘grey zone of population differentiation’, named to signify those cases common in the marine realm, where the split among population is too recent or too faint to be detected using classical genetic markers. Here, samples collected across the majority of the global range of blue shark were sequenced (using a specific genome scan method named DArTseq) and screened through genome scan using 37,655 single nucleotide polymorphisms. Significant differences distinguished locations from the northern (Mediterranean and North Atlantic) vs. southern (southeastern Atlantic, Indian Ocean and southwestern Pacific) oceanic regions. Furthermore, FST values were significant, albeit low, between locations from distinct regions within the Atlantic Ocean (northern vs. northeastern vs. southeastern Atlantic). In addition, FST values were significant between these Atlantic locations and Mediterranean, Indian, and Pacific locations. These results illustrate the power of genome scans to delineate independent populations in marine species and to accurately identify distinct management units.