The three countries of the Benguela Current Large Marine Ecosystem (BCLME), namely Angola, Namibia and South Africa, have committed to implementing ecosystem-based management (EBM) including an ecosystem approach to fisheries (EAF) in the region, to put in practice the principles of sustainable development in ocean-related matters. There is also recognition of the need for marine spatial planning (MSP) as a process for informing EBM with regard to the allocation and siting of ocean uses so that ecosystem health is ensured and trade-offs between ecosystem services are appropriately dealt with. Marine spatial planning is both an integrated and an area-based process, and this paper produces a spatial characterisation of the BCLME for achieving a common basis for MSP in the region, focusing on the oceanography, biology and fisheries. Recognising spatial variation in physical driving forces, primary and secondary production, trophic structures and species richness, four different subsystems are characterised: (1) north of the Angola-Benguela Front, (2) from the Angola-Benguela Front to Luderitz, (3) from Luderitz to Cape Agulhas, and (4) from Cape Agulhas to Port Alfred on the south-east coast of South Africa. Research and monitoring requirements of relevance for MSP and EBM in the region are identified, focusing on understanding variability and change, including with regard to the boundary areas identified for the system. To this end, 14 cross-shelf monitoring transects are proposed (including seven that are already being monitored) to estimate fluxes of biota, energy and materials within and between the subsystems. The usefulness of models for understanding ecosystem variability and changes is recognised and the need for fine-scale resolution of both sampling and modelling for adequate MSP as input to EBM for the often-conflicting interests of conserving biodiversity, and managing fisheries, recreation, offshore oil and gas exploration and exploitation, offshore mining and shipping routes, is emphasised.