For Traditional Owners, Country is an integrated ecological, human and spiritual universe which spans land and sea. Today Sea Country is separated legally and administratively from terrestrial Country, and is intersected by a range of statutory arrangements. For Marra Traditional Owners, Northern Territory and Commonwealth fisheries, conservation, cultural heritage and land rights legislation interact in complex ways. Historically, this has amongst other things created barriers to Marra having a strong voice in how their Sea Country is managed. We report on work developing a Traditional Owner-led management schema for Marra Sea Country. We explain what Marra identify as important about their Sea Country, and the threatening processes they observe in a contemporary setting. We then speak to our planning process, which seeks to recognise the dual authorities of government and Traditional Owners. Finally, we discuss the interagency collaborations being fostered as Marra enlist support from various government agencies to implement their management approach across a complex statutory environment. We believe that by starting with Traditional Owner’s deep knowledge of Country, the effectiveness of management can be improved. We explore the scientific, planning and policy innovations this work represents, and the principles which underpin robust Indigenous-led marine management collaborations.