The deep sea, comprising approximately 95% of the world ocean volume, is by far the largest cumulative habitat on earth. It has historically been understudied and represents the largest data gap in ecology. The deep sea is home to an enormous diversity of ecosystems, from the three-dimensional fluid space of the pelagic realm to the seamounts, trenches and vast plains of the seafloor. Despite the high pressures, almost perpetual darkness, and low food availability that characterizes much of the deep sea, it nonetheless harbors an incredible abundance and diversity of specialized animal life. Technological developments made in recent decades are increasing our access to the deep sea and are delivering exciting new insights into the dynamic nature of deep-sea ecosystems, and their role in connecting the oceans to coastal and terrestrial ecosystems. However, the increasing human footprint in the deep sea is also increasingly apparent. In this article, we provide a general summary of the main ecological divisions of the deep-pelagic and benthic realms; discuss some of the major morphological, sensory and trophic adaptions shown by the deep-sea metazoan fauna, and conclude with a discussion of ecosystem functioning and human threats to deep-sea ecosystems.