A high-resolution molecular organic geochemical study of sediments in the anoxic Cariaco Basin indicates significant changes in primary productivity and planktonic community structure associated with the transition from the Younger Dryas to the Holocene. Variations in climate conditions over the past 12 14C kyr have induced large-scale changes in upwelling intensity, which directly affected levels of primary productivity as reflected in accumulation rates of bulk productivity proxies. Concentrations and accumulation rates of sterol and alkenone biomarkers have been used to identify how productivity changes affected the structure of the planktonic ecosystem. A shift in the dominant primary producer from diatoms (Younger Dryas) to coccolithophores (Holocene) is identified. If productivity and ecosystem variations like those identified in the tropical upwelling zone of the Cariaco Basin region, occur throughout the tropical oceans, they have the potential to affect global climate through perturbations in the biogeochemical cycle of carbon.