Ecosystem-based management (EBM) in the ocean is a relatively new approach, and existing applications are evolving from more traditional management of portions of ecosystems. Because comprehensive examples of EBM in the marine environment do not yet exist, we first summarize EBM principles that emerge from the fisheries and marine social and ecological literature. We then apply those principles to four cases in which large parts of marine ecosystems are being managed, and ask how including additional components of an EBM approach might improve the prospects for those ecosystems. The case studies provide examples of how additional elements of EBM approaches, if applied, could improve ecosystem function. In particular, two promising next steps for applying EBM are to identify management objectives for the ecosystem, including natural and human goals, and to ensure that the governance structure matches with the scale over which ecosystem elements are measured and managed.