Early Palaeocene through early Eocene silicoflagellate assemblages were examined from five southern subtropical through subpolar deep-sea sites: DSDP Holes 208 and 524, and ODP Holes 700B, 752A, and 1121B. For each site, the taxonomic composition of the silicoflagellate assemblage is documented in detail; Pseudonaviculopsis gen. nov., Dictyocha castellum sp. nov. and Stephanocha? fulbrightii sp. nov. are proposed, along with several new combinations. More importantly, however, these observations enable a considerable refinement to the existing Palaeocene–Eocene silicoflagellate biostratigraphic zonation that for the first time uses datums calibrated to the Geomagnetic Polarity Timescale. The Corbisema aspera Interval Zone occurs immediately above the K/Pg boundary and is here described from Seymour Island. The Corbisema hastata Partial Range Zone extends from near the K/Pg boundary to late early Palaeocene and has been observed in Hole 208. The Pseudonaviculopsis disymmetrica Acme Zone occurs in Holes 208 and 700B. The Dictyocha precarentis Partial Range Zone, observed in Holes 208, 700B, 752A and 1121B, is subdivided into D. precarentis, Naviculopsis primativa, N. cruciata and Pseudonaviculopsis constricta subzones. The Naviculopsis constricta Partial Range Zone occurs in Holes 524, 700B, 752A and 1121B. This study is also the first to consider syn- and/or diachroneity in Palaeogene silicoflagellate biostratigraphy.