This dataset comprises fossil time series data of coccolith absolute and relative abundance for the species Gephyrocapsa kamptneri (including its morphotypes), and for Florisphaera profunda in the Late Quaternary for microevolutionary studies. The data were collected at approximately 10,000-year resolution from clayey foraminiferal nannofossil ooze sediments that were recovered from the deep-sea drilling site: ODP Leg 154 Site 925 (Equatorial Atlantic Ocean) using scanning electron microscopic analyses. Each sediment sample was brought into suspension using low-carbonated water, ultrasonicated for 5–10 seconds, wet-sieved to remove larger particles and settled onto a round cover slip that was oven-dried. Cover slips were mounted onto aluminium stubs using a double-sided adhesive carbon tape. Stubs were sputter-coated with gold and examined under an electron microscope.