We report the first evidence of Hg content in marine sediments changing in connection with the climate-driven changes in ocean stratification during the Quaternary Period based on core samples from ODP Hole 1006A off Great Bahama Bank in the Caribbean Sea. The Hg content ranged from 5.9 to 60.7 ng/g with an average value of 33.1 ng/g during 350 and 1330 ka and changed inversely with δ18Oplanktonic values. The change in Hg content was positively correlated with total organic carbon (TOC) content, indicating connections between the δ15Norg and δ13Corg values of organic matter and the absolute abundance of a deep-dwelling calcareous nannoplankton (Florisphaera profunda). The marine Hg is thought to have been incorporated into the organic matter produced by deep-dwelling phytoplankton. Based on these results, we propose a mechanism by which marine Hg can collect in a thermocline formed in the stratified lower photic zone. Mercury content and nannoplankton assemblage in marine sediment provide information about the extent of stratification of the oceanic photic zone and the role of surface- and deep-dwelling phytoplankton in producing marine organic matter and changing its δ15Norg and δ13Corg values.