Paleoceanographic reconstructions in the Caribbean Sea during past climate transitions, namely the Late Oligocene to Early Miocene (up to the Miocene Climatic Optimum and Monterey Excursion) are crucial to understanding the effects of the Eastern Pacific interchange with the Atlantic Ocean. Studies of the planktonic domain in the Yucatan Basin during the Early Miocene are limited, with most Caribbean research focused on reconstructing the series of events that precede the final closure of the Isthmus of Panama in the Early Pliocene. Furthermore, paleoceanography of the Yucatan Basin is largely unrefined during this time, even though it is an important transition for ocean gateways, and development of Atlantic deepwater and Atlantic Meridional Overturning Current (AMOC), driving global ocean circulation. Here we conduct a relative percent abundance analysis of calcareous nannofossils and stable isotopes from bulk sediment of drill cores spanning the Upper Oligocene to Lower Miocene in the central Yucatan Basin, collected by the Ocean Drilling Program Leg 165 at Site 998 Hole A. Nannofossil assemblage data record a shift from a eutrophic to oligotrophic system ∼19.2–17.65 Ma. Eutrophic taxa (Reticulofenestra spp. and Cyclicargolithus floridanus) decline at ∼20.23 Ma, while oligotrophic taxa (discoasters and sphenoliths) increase as stable carbon isotope values decline. The palaeoecological turnover coincides with a possible restriction in the Central American Seaway (CAS) ∼20.7–21 Ma. Population dynamics of the Hole 998 A nannofossil assemblage track with global declines in C. floridanus relative abundance between ∼20.2 to ∼20.5 Ma, followed by a subsequent decrease in Reticulofenestra spp. These data suggest water mass stratification in the Yucatan Basin during the Early Miocene ∼19.2–17.65 Ma, likely due to restriction of the CAS.