Caribbean paleoproductivity in the late Miocene to late Pliocene changed in response to the uplift of southern Central America and the constriction to complete closure of the Panama seaway. We analyze large-scale patterns of productivity from 6 to 2 Ma using foraminifera and other data from ODP Leg 165, Site 999. Several proxies are compared: a primary paleoproductivity value based on carbonate mass accumulation rates (PpP), benthic foraminifera accumulation rates (BFAR) of the >63-micron fraction, C/N ratio, and relative abundance of Epistominella exigua. Primary paleoproductivity rapidly decreased from 5.8 to 4.75 Ma as upwelling gradually decreased. From 4.75 to 4.0 there was a period of slight increase in paleoproductivity, followed by a slight but gradual decrease until 2 Ma. Thus, there was an overall decrease in primary paleoproductivity from late Miocene to Pliocene time, resulting in the oligotrophic conditions that currently prevail in the Caribbean Sea. We compare the paleobiodiversity of benthic foraminifera along a shallow (inner neritic) to deep (middle bathyal) transect in relation to the changes in productivity combining materials from the Panama Paleontology Project and the ODP Leg 165.