We reinvestigated the standard calcareous nannofossil and diatom biostratigraphy zonations from Deep Sea Drilling Project (DSDP) Leg 41 Holes 366 and 369A in the eastern equatorial Atlantic Ocean in order to determine the geologic ages for the low-latitude diatom zonation. Applying the ages of nannofossil zonations to diatom ones, the ages of several diatom bioevents (first occurrence, FO) which determine the biozones of DSDP Holes 366 and 369A are evaluated as follows; FOs of Baxteriopsis brunii (ca. 38.1 Ma), Coscinodiscus excavatus (ca. 33.6 Ma), Cestodiscus reticulatus (ca. 32.9 Ma), Rocella vigilans (ca. 29.8 Ma), Rossiella symmetrica (ca. 29.5 Ma) and Bogorovia veniamini (ca. 28.3 Ma). These ages may be applicable not only for these holes but also for biostratigraphic studies of other holes which contain Paleogene diatoms. Moreover, this paper describes the taxonomy and stratigraphic ranges of marine diatom Chaetoceros resting spores from DSDP Holes 366 and 369A, including two new morpho-species (Vallodiscus truncatuhis Suto sp. nov. and Xanthioisthmus fortii Suto sp. nov.) and its allied species with synonymy lists, light microscopic observations and several key references for each taxon. As the results of counting of each diatom taxon, it was clear that the sedimentation rate and Chaetoceros resting spore abundances and diversities changed abruptly in the earliest Oligocene (ca. 32 Ma). During the separation of the South American and African continents from the Late Cretaceous to earliest Oligocene, a passage arose that acted for the transfer of Antarctic Bottom Water and modulated the bottom current velocities. The southward bottom water and the passage influenced the sedimentation rate and upwelling of nutrient-rich deeper waters stimulated marine productivity and ecology of Chaetoceros across the late Eocene to early Oligocene.