Assessing the relative contribution of local diversity to regional biodiversity may be the key to understanding large-scale and even global patterns in species diversity. Here, the contribution of habitat heterogeneity of cold seeps at three spatial scales [micro-scale (ms), macro-scale (10 to 100s of ms), and mega-scale (10 to 100s of km)] to the total nematode biodiversity (genus level) along the Norwegian continental margin is evaluated. Due to the development of higher resolution bathymetry and increased bottom sampling in recent years, continental margins, once regarded as monotonous landscapes, are now acknowledged to have a high degree of habitat complexity and diversity. By calculating the additive partitioning of gamma diversity in alpha and beta fractions, we examined to what extent habitat diversity of seep sites significantly increases the nematode genus composition and diversity at different spatial scales. Siboglinidae patches and control sediments yielded comparably high levels of nematode genus richness. They exhibited low turnover rates within and across the different seep sites. In contrast, the bacterial mats at Håkon Mosby Mud Volcano (HMMV) and the reduced sediments at the Nyegga pockmarks harboured genus-poor nematode communities with an equally high dominance of one or two species, which were different for each seep. Different habitats, in particular at the HMMV, contributed significantly to the seep nematode richness. This study demonstrates that the presence of distinct habitat types within multiple seep sites contributes to the high diversity of nematode communities inhabiting the seeps in the Norwegian deep sea.