The diversity of Arctic (off Northeast Greenland) and Antarctic (Weddell and Bellingshausen Seas) megabenthic assemblages was compared using underwater video at depths of between 30 and 550 m. The number of taxa found at each station was highest on the Weddell Sea shelf, which can be interpreted as being a result of the long isolation of the Antarctic fauna. However, the within-habitat (alpha-) diversity of these assemblages did not differ significantly from those off Greenland or in the Bellingshausen Sea at a comparable depth range. This is apparently due to the similarity in dominance patterns, independent of species numbers. The Bellingshausen Sea and Greenland stations exhibited similar between-habitat (beta-) diversity patterns, while the Weddell Sea stations showed a slightly different beta- and a pronounced higher overall diversity. This can be partly explained by the development of an epibiotic behaviour by several Antarctic suspension feeding species. On the shallow shelf off Northeast Greenland the alpha-diversity was found to be low but the beta-diversity was relatively high. This may be due to the relatively high impact of physical and biological disturbances at shallower depths and the more stable environmental conditions in the deeper parts of all three investigation areas.