The calcareous nannoplankton underwent a major diversification between 60 Ma and 61 Ma with the appearance of two important Cenozoic genera, Fasciculithus and Sphenolithus. We have studied the evolution of these genera at four deep-sea sites using a combination of biostratigraphic and assemblage analyses. Our data show that the first appearances of both genera are time transgressive between sites by up to 1 myr, suggesting that these taxa were highly specialized or that ocean environments were heterogeneous. The interval of diversification coincided with a major turnover among nannoplankton assemblages involving an increase in taxa adapted to oligotrophic environments and a decrease in those suited to mesotrophic settings. The opening of niche space for oligotrophs such as Fasciculithus and Sphenolithus coincides with the radiation of oligotrophic planktonic foraminifers, including the genus Morozovella. The appearance of both groups occurred about 1 myr after the recovery of the biologic pump following its collapse at the Cretaceous–Paleocene mass extinction. This suggests that increased export efficiency stripped nutrients from surface waters, causing a major upheaval among marine food webs.