Continental margins, where land becomes ocean and plunges to the deep sea, provide valuable food and energy resources, and perform essential functions such as carbon burial and nutrient cycling. They exhibit remarkably high species and habitat diversity, but this is threatened by our increasing reliance on the resources that margins provide, and by warming, expanding hypoxia and acidification associated with climate change. Continental margin ecosystems, with environments, constituents and processes that differ from those in shallow water, demand a new focus, in which ecological theory and experimental methods are brought to bear on management and conservation practices. Concepts of disturbance, diversity-function relationships, top-down versus bottom-up control, facilitation and meta-dynamics offer a framework for studying fundamental processes and understanding future change.