The great variety of geological and hydrological conditions in the deep sea generates many different habitats. Some are only recently explored, although their true extent and geographical coverage are still not fully established. Both continental margins and mid-oceanic seafloors are much more complex ecologically, geologically, chemically and hydrodynamically than originally thought. As a result, fundamental patterns of species distribution first observed and explained in the context of relatively monotonous slopes and abyssal plains must now be re-evaluated in the light of this newly recognized habitat heterogeneity. Based on a global database of nematode genus composition, collected as part of the Census of Marine Life, we show that macrohabitat heterogeneity contributes significantly to total deep-sea nematode diversity on a global scale. Different deep-sea settings harbour specific nematode assemblages. Some of them, like coral rubble zones or nodule areas, are very diverse habitats. Factors such as increased substrate complexity in the case of nodules and corals seem to facilitate the co-existence of a large number of genera with different modes of life, ranging from sediment dwelling to epifaunal. Furthermore, strong biochemical gradients in the case of vents or seeps are responsible for the success of particular genera, which are not prominent in more typical soft sediments. Many nematode deep-sea genera are cosmopolitan, inhabiting a variety of deep-sea habitats and oceans, whereas only 21% of all deep-sea genera recorded are restricted to a single habitat. In addition to habitat heterogeneity, regional differences are important in structuring nematode assemblages. For instance, seeps from different regions yield different genera that thrive on the sulphidic sediments. This study also shows that many areas and habitats remain highly under-sampled, affecting our ability to understand fully the contribution of habitat heterogeneity versus regional differences to global nematode diversity.