Variations in the accumulation rate and preservation of late Pliocene calcareous nannofossils from the eastern equatorial Pacific Ocean are studied. Increases in the accumulation rate of nannofossils, are related to changes in paleoproductivity which in turn are linked to paleoceanographic change. Maxima in fluxes of nannofossils observed from 3.50 to 3.40 and 3.10 to 2.65 Ma are interpreted as periods of high paleoproductivity. The nannofossil accumulation rate at Site 849, an area of oceanic divergence, on average is 10 times higher than that recorded at Site 852 (convergence area). Moreover, dissolution intensity is greater at Site 852. Times of greater dissolution at Site 852, characterized by high percentages of asteroliths, generally coincide with times of lower nannofossil accumulation rates at Site 849. Therefore, we assume that productivity and dissolution may be inversely related because the carbonate compensation depth (CCD) and the lysocline are deeper in the equatorial divergence region as a result of the higher carbonate supply in this region. The accumulation rate of asteroliths have a similar rank in both sites, allowing us to conclude that this group is relatively more abundant in the region of lower productivity, whereas it has been diluted in the higher productivity area. Aremarkable event is identified at 3.20 Ma in both sites. The reentry of the cool water species Coccolithus pelagicus coincides with a shoaling of the CCD, which may indicate a major paleoceanographic change in the eastern equatorial Pacific Ocean. Northward and southward currents may have been established or intensified at this age, introducing cool elements in the nannofossil assemblage at the same time that the Atlantic-Pacific connection become restricted through the Panamanian Corridor. The accumulation rate of Pseudoemiliania lacunosa follows a similar trend as that of C. pelagicus. Its high fluxes during globally recognized cool periods lead us to infer that it is linked to low-temperature surface waters. Between 4 and 2 Ma, a similar pattern of nannofossil accumulation rates is observed in the divergence and convergence areas, suggesting that a general model explains any variations in eastern equatorial Pacific Ocean.