Nannoplankton assemblages at Ocean Drilling Program Site 690 (Maud Rise, Weddell Sea) experienced an abrupt and dramatic transformation at the onset of the Paleocene‐Eocene Thermal Maximum (PETM) at ∼55 m.y. The major assemblage shift suggests a change from colder, more productive surface waters to warmer, more oligotrophic conditions. Significant restructuring of assemblages during the later part of the PETM indicates that nannoplankton communities were not stable and that surface water conditions changed, although they remained warm and oligotrophic. Combined with benthic foraminiferal assemblage data, nannoplankton assemblage results suggest increased sequestration of nutrients in shelf environments and starvation of the open ocean. Although the PETM was a short‐lived event, it appears to have had long‐term effects on nannoplankton, leading to the extinction of Fasciculithus, a dominant Paleocene genus.