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Genetic markers provide a natural tagging approach to assess the degree of gene flow and population connectivity across a species distribution. We investigated the genetic structure of black bream <jats:italic>Acanthopagrus butcheri<\/jats:italic> across its entire distribution range in Australia, as well as regional scale gene flow across south\u2010eastern Australia by undertaking a comprehensive analysis of the populations in estuaries across the region. We applied genome\u2010wide sampling of single\u2010nucleotide polymorphism (SNP) markers generated from restriction site\u2010associated DNA sequencing. Genetic structure and potential gene flow was assessed using principal component analyses and admixture analyses (<jats:italic>STRUCTURE<\/jats:italic>). Using 33,493 SNPs, we detected broad scale genetic structuring, with limited gene flow among regional clusters (i.e. Western Australia, South Australia and western Victoria; and eastern Victoria, Tasmania and New South Wales). This is likely the result of unsuitable habitats, strong ocean currents (e.g. the Leeuwin Current and the East Australian Current), large water bodies (e.g. Bass Strait) and known biogeographical provinces across the continent. Local\u2010scale genetic structuring was also identified across the south\u2010eastern Australian estuaries sampled, reflecting that the coexistence of both migratory and resident individuals within populations (i.e. partial migration), and the movement of fish into coastal waters, still results in strong philopatry across the region. Instances of movement among estuaries at this spatial scale were primarily found between adjacent estuaries and were likely attributed to lone migrants utilising inshore coastal currents for movement beyond nearby habitats. Targeting SNP markers in <jats:italic>A.\u2009butcheri<\/jats:italic> at this continental scale highlighted how neither spatial proximity of estuaries nor black bream's ability to move into coastal waters reflects increased gene flow. Overall, our findings highlight the importance of location\u2010specific management.<\/jats:p>","DOI":"10.1002\/ece3.10989","type":"journal-article","created":{"date-parts":[[2024,3,18]],"date-time":"2024-03-18T07:54:20Z","timestamp":1710748460000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Strong philopatry in an estuarine\u2010dependent fish"],"prefix":"10.1002","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5917-1774","authenticated-orcid":false,"given":"Koster G.","family":"Sarakinis","sequence":"first","affiliation":[{"name":"Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide  Adelaide South Australia Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9843-9465","authenticated-orcid":false,"given":"Patrick","family":"Reis\u2010Santos","sequence":"additional","affiliation":[{"name":"Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide  Adelaide South Australia Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5448-3226","authenticated-orcid":false,"given":"Stephen C.","family":"Donnellan","sequence":"additional","affiliation":[{"name":"South Australian Museum  Adelaide South Australia Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3372-5297","authenticated-orcid":false,"given":"Qifeng","family":"Ye","sequence":"additional","affiliation":[{"name":"South Australian Research and Development Institute Aquatic and Livestock Sciences  Adelaide South Australia Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1352-9483","authenticated-orcid":false,"given":"Jason","family":"Earl","sequence":"additional","affiliation":[{"name":"South Australian Research and Development Institute Aquatic and Livestock Sciences  Adelaide South Australia Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7680-2240","authenticated-orcid":false,"given":"Bronwyn 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