We are beginning to appreciate that the origin of the modern Antarctic marine fauna is related to a series of key events throughout the Cenozoic era. In the first of these, the mass extinction at the Cretaceous–Palaeogene boundary (66 Ma) reset the evolutionary stage and led to a major radiation of modern taxa in the benthic realm. Although this took place in a greenhouse world, there is evidence to suggest that the radiation was tempered by the seasonality of primary productivity, and this may be a time‐invariant feature of the polar regions. Although there could well have been a single, abrupt extinction event at c. 34 Ma, there is also evidence to suggest a phased extinction of various taxa over a period of millions of years. Important new molecular phylogenetic data are indicating that a wide variety of both benthic and pelagic taxa radiated shortly after a second major phase of cooling at c. 14 Ma. Such a phenomenon is linked to a series of major palaeoceanographic changes, which in turn led to a proliferation of diatom‐based ecosystems. Although the modern benthic marine fauna can be traced back some 45–50 Myr, a substantial component of the modern pelagic one may be less than 14 Myr old. The latter is also characterized by assemblages of high abundance but comparatively low species richness and evenness. A distinctive signature of low diversity but high dominance within Antarctic marine assemblages was maintained by the interplay between temperature and primary productivity throughout the Cenozoic.