School Shark (Galeorhinus galeus) is a semi-pelagic, highly migratory species with a widespread distribution in temperate waters. Formerly an important component of the Australian shark fishery, Australian School Shark stocks have been depleted to below 20% of their virgin biomass. The recovery management plan for this species has impacted other shark fisheries where School Sharks represent a significant bycatch, for example, in the Gummy Shark (Mustelus antarcticus) fishery. This has prompted renewed efforts to develop management strategies through better understanding of stock structure and connectivity of School Shark populations in Australian and New Zealand waters. To date, molecular based studies on Australasian School Shark population structure yielded contrasting results and have suggested Australian and New Zealand individuals could be clustered and managed as either one or multiple populations. Management practices in Australasian water reflect this uncertainty where current management considers two separate Australian and New Zealand stocks. However, more recently there has been discussion of managing them as a single stock for assessment purposes. Accurate determination of stock structure and population connectivity is crucial to inform this decision. In this study, we assess of the genetic composition and population connectivity between Australian and New Zealand School Sharks using genome-wide single nucleotide polymorphisms (SNP). Between 2009 and 2015, 188 neonate and adult individuals originating from Australia (South Australia, West Tasmania and South Tasmania) and New Zealand were collected and genotyped. Both neutral and outlier loci were analysed to detect fine-scale signals of connectivity and local adaptation. Our results indicate there may be a lower level of genetic connectivity than previously assumed with outlier loci potentially indicating locally adapted groups at the regional level. Further investigations of population structure among Australian and New Zealand sampling locations could help to guide management strategies developed for the School Shark and Gummy Shark fisheries.