The deep–ocean floor extends over two thirds of the world’s surface, and is thus the largest benthic habitat on the planet. The myth of depauperate deep–sea communities was debunked in the 1960s by the pioneering work of Hessler and Sanders (Hessler and Sanders, 1967; Sanders and Hessler, 1969) with their newly developed epibenthic sled. They showed deep–sea diversity to be equivalent to that found in shallow tropical marine habitats, and greater than in boreal tropical and temperate estuaries and boreal shallow marine habitats. They also identified depth as the most important correlate of faunal abundance and as a factor driving community composition. Technological developments over the last 50 years have continued to drive advances in our knowledge of this diverse and heterogeneous biome. Efforts to enumerate and catalogue the diversity have led to claims of high levels of endemism (E.g., Wolff, 1970; Belyaev, 1989; Stocks and Hart, 2007; Ebbe et al., 2010) but poor knowledge of the global species pool and uneven regional sampling probably artifactually inflate these estimates (e.g., Rowden et al., 2010; Clark et al., 2012). The term “deep sea” encompasses many different habitats, shaped by their physical characteristics – geographic location, slope, depth – which determine their biodiversity and dominant fauna, and their connectivity. Here, we first explore biogeography and phylogeography of these habitats, and consider some of the molecular work which is testing various biogeographic schemes. We then look briefly at some of the abiotic parameters that characterise various deep-sea habitats. Interactions in the deep sea are many, but they are often not well investigated. Few studies on competition and predation match the detail of those conducted in shallow waters. In constrast, symbioses have been better researched, being the basis of much productivity at hydrothermal vents and cold seeps, and highly prevalent in filter-feeder dominated habitats on the steep slopes of submarine canyons and seamounts. Finally we explore where sufficient bodies of work exist to allow us to infer processes from patterns, and conclude that very much more work on ecological interactions in the deep-sea is needed.