The ‘deep sea’ encompasses a broad range of habitats that differ greatly in their assemblages and ecosystem functioning. Habitats may be described by a combination of environmental factors (e.g., depth, slope) and biotic factors (e.g., source of primary productivity). We review recent attempts to define deep-sea biogeographic provinces based on spatial and temporal variations in oceanographic conditions, and consider potential boundaries to distributional ranges, in particular habitats based on recent phylogeographic studies. We briefly discuss abiotic interactions in various habitats, noting the particular influence of local hydrodynamics. We consider competition and predation at whale falls and hydrothermal vents, discuss symbiotic interactions particularly with respect to deep-sea corals, which are particularly prevalent in submarine canyons and seamounts, and consider the difficulties of inferring processes from patterns.