Pelagic carbonates constitute the majority of the ocean sediments, particularly since the Jurassic, and record climatic and oceanic changes. Cenozoic sediments record glacial and interglacial periods, as well as thermal maxima, such as the PETM (Paleocene-Eocene Thermal Maximum) at ca. 56 Ma or the MECO (Middle Eocene Climatic Optimum) that dates back to ca. 40 Ma. The Paleogene period shows variations in seawater temperature and atmospheric CO2, as well as fluctuations of the carbonate compensation depth (CCD). In order to understand the actions and feedbacks between climate (regulated amongst others by temperature, partial pressure of CO2, and atmospheric belts), CCD fluctuations and pelagic carbonate producers, the fluxes, assemblages and sizes of calcareous nannofossils were studied from sediments dated between 48 and 39 Ma, including the MECO interval. Calcareous nannofossils were analysed in from the ODP (Ocean Drilling Project) Leg 198 Site 1209A, Shatsky Rise located in the tropical Pacific. The previously proposed age model for Site 1209 has been slightly modified based on new calcareous nannofossil biostratigraphy recalibrated according to the GTS 2012. In a long-term perspective, calcareous nannofossil assemblages and taxa size show significant changes during the middle Eocene. Our data suggest that relatively oligotrophic conditions occurred between 48 and 45 Ma, interrupted by higher trophic conditions between 45 and 39 Ma, although oligotrophy occurred again during the MECO. Discoaster spp. show smaller sizes from 48 to 39 Ma, mirroring the global temperature decrease. At 40 Ma, during the MECO, large-sized reticulofenestrids with a peak of Reticulofenestra umbilicus (\textgreater 14 mu m) occurred, whereas smaller but heavily calcified Dictyococcites spp. peak in the aftermath of the MECO. Calcareous nannofossil fluxes show a significant increase with respect to background values during the CAEs (Carbonate Accumulation Event), although they are low during the MECO. Calcareous nannofossil fluxes seem to have had important impact on the oceanic carbon cycles, by creating a carbonate flux to the ocean interior, likely contributing to the CCD deepening.