The United Nations Convention on Law of the Sea (UNCLOS) (United Nations 1982) came into effect in 1994. Signatory nations have substantial management obligations for conservation of marine natural resource and ecosystems. In this paper we discuss the challenges of defining and monitoring biodiversity at scales required for management of marine ecosystems. Australia's area of immediate responsibility under UNCLOS covers an area of 11 million sq km with further linked responsibilities for an estimated area of 5.1 million sq km of continental shelf. This presents substantial data challenges for development and implementation of management. Acoustic seabed mapping is providing substantial information on seabed surface geology and topography and provides a surrogate basis for describing benthic habitat and seabed communities that have critical roles in marine food chains. The development of the Integrated Marine and Coastal Regionalisation of Australia (IMCRA 4.0, 2006) has provided a basis for planning marine biodiversity and resource management but the biological habitat interpretation of geological data is based very largely on demersal fish data. It is recognised in IMCRA 4.0 (2006) that revision and refinement of regionalisation requires further work in the areas of data coverage, ecosystem understanding and ecosystem surrogates and conceptual classification models. In this paper we discuss Australian experience highlighting problems and issues of relevance for scientifically based management of marine natural resource and ecosystems elsewhere in the world.