Processes regulating population connectivity are complex, mediated by species movement and gene flow, and play a key role in shaping fisheries and environmental management actions. The estuarine-dependent black bream (Acanthopagrus butcheri) exhibits partial migration and is distributed across southern Australia, from Western Australia to New South Wales, including Tasmania. Yet, we still have a limited understanding of this species genetic connectivity among estuaries. The aim of this study was to assess population structure and genetic connectivity across the entire species distribution range. Black bream were sampled from 26 sites across Western Australia, South Australia, Victoria, New South Wales and Tasmania to determine (1) if populations differed genetically and (2) the degree of gene flow present across all southern Australia. Next-generation RAD-sequencing was utilised to target Single-Nucleotide Polymorphisms (SNP) genetic markers. To assess population structure and gene flow a combination of PCAs, admixture models and isolation-by-distance tests were completed. Results show clear population structure across southern Australia, including at regional and local scales. The strong genetic variation and reduced gene flow across black bream populations suggests a location-specific approach to managing this commercially important species may need to be considered.