This dataset comprises of fossil time series data for the species Gephyrocapsa undulata (including its morphotypes) and Florisphaera profunda over the last 300,000 years. The data were collected at approximately 10,000-year resolution from Quaternary clayey foraminiferal nannofossil ooze sediments recovered from five deep-sea drilling sites: ODP Leg 162 Site 982; ODP Leg 154 Site 925; ODP Leg 138 Site 846; and DSDP Leg 68 Site 502. Absolute and relative abundance data and coccolith identification were based on scanning electron microscopic analyses.