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Continuing pressures from human activities have harmed the health of ocean ecosystems, particularly those near the coast. Current management practices that operate on one sector at a time have not resulted in healthy oceans that can sustainably provide the ecosystem services humans want and need. Now, adoption of ecosystem-based management (EBM) and coastal and marine spatial planning (CMSP) as foundational principles for ocean management in the United States should result in a more holistic approach. Recent marine biogeographical studies and benthic habitat mapping using satellite imagery, large-scale monitoring programs, ocean observation systems, acoustic and video techniques, landscape ecology, geographic information systems, integrated databases, and ecological modeling provide information that can support EBM, make CMSP ecologically meaningful, and contribute to planning for marine biodiversity conservation. Examples from coastal waters along the northeast coast of the United States from Delaware Bay to Passamaquoddy Bay, Maine, illustrate how benthic biogeography and bottom seascape diversity information is a useful lens through which to view EBM and CMSP in nearshore waters. The focus is on benthic communities, which are widely used in monitoring programs and are sensitive to many stresses from human activities.