The diversity of Arctic (off northeast Greenland) and Antarctic (Weddell and Bellingshausen Seas) megabenthic assemblages was compared using underwater video at depths 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 (α) diversity of the Weddell Sea assemblages did not differ significantly from those off Greenland or in the Bellingshausen Sea in a comparable depth range. This is apparently due to the similarity in dominance patterns, independent of species numbers. The Bellingshausen Sea and Greenland Sea stations exhibited similar between-habitat (β) diversity patterns, while the Weddell Sea stations showed a slightly higher β-diversity 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 α-diversity was low, but the β-diversity was relatively high compared to the other areas sampled. 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 3 investigation areas.