The Eastern School Whiting (Sillago flindersi) is an inshore demersal species that is endemic to south-eastern Australian ocean waters to a depth of about 100 m, from southern Queensland to north-eastern Tasmania and west along the mainland coast to Anxious Bay in South Australia. Previous work examining genetic stock structure with allozyme markers suggested a weak division in the vicinity of Forster, central NSW. However, the hypothesis of a single, genetically diverse panmictic stock could not be rejected, and the species has been assessed as a single biological stock. Given the complex spatial fisheries management arrangements for trawl fisheries in south-eastern Australia there is a need to resolve stock structure for cross-jurisdictional stock assessments and harvest strategy management. Here we re-examine the genetic structure of S. flindersi across its range, with next-generation sequencing of highly variable single nucleotide polymorphism (SNP) markers. The findings are not concordant with historical results. Rather there is strong support for all locations in NSW and eastern Victoria forming a single panmictic population, a clear division between the mainland and Tasmanian samples, and a weak indication of a second division within the Victorian coastline.