Ecosystem-based management (EBM) and the related concept of large marine ecosystems (LMEs) are sometimes criticized as being too broad for many management and research applications. At the same time, there is a great need to develop more effectively some substantive scientific methods to empower EBM. Marine habitat mapping (MHM) is an example of an applied set of field methods that support EBM directly and contribute essential elements for conducting integrated ecosystem assessments. This manuscript places MHM practices in context with biodiversity models and EBM. We build the case for MHM being incorporated as an explicit and early process following initial goal-setting within larger EBM programmes. Advances in MHM and EBM are dependent on evolving techno- logical and modelling capabilities, conservation targets, and policy priorities within a spatial planning framework. In both cases, the evolving and adaptive nature of these sciences requires explicit spatial parameters, clear objectives, combinations of social and scien- tific considerations, and multiple parameters to assess overlapping viewpoints and ecosystem functions. To examine the commonal- ities between MHM and EBM, we also address issues of implicit and explicit linkages between classification, mapping, and elements of biodiversity with management goals. Policy objectives such as sustainability, ecosystem health, or the design of marine protected areas are also placed in the combined MHM–EBM context.