Marine sediments from the Western and Eastern South Atlantic continental margins are used to reconstruct mercury (Hg) accumulation over the last glacial/interglacial cycle. Sediment core GL-1248, collected from the continental slope off northeastern Brazil, and sediment core ODP1077, retrieved from the Congo deep-sea fan area, both dated to the last 128 ka and 130 ka respectively. Mercury concentrations in GL-1248 ranged between 14.95 and 69.43ng/g, and varied with periodicities of 56 ka and 900 yr suggesting the presence of glacial-interglacial changes and millennial-scale variability respectively. Parallel trends of Hg and XRF-Fe plots suggest that following atmospheric Hg deposition onto the continent, Hg is incorporated with iron (Fe) minerals before transportation and eventual immobilization at the NE Brazil continental slope. Mercury concentrations in ODP1077 varied significantly, having concentrations between 23.12 ng/g and 256 ng/g, and its plot exhibits an anti-phase pattern with the Fe/Ca ratio plot, that distinguishes between periods of increased and decreased terrigenous material delivery. This inverse trend in the plots of mercury concentration and Fe/Ca ratio shows that during periods of increased (decreased) terrigenous material delivery, less (more) mercury accumulates in the marine sediment. Although Hg concentration is poorly correlated with total organic carbon (TOC), it correlates positively with XRF-Ca implying that marine organic matter played a significant role in mercury distribution and accumulation in the ODP1077 marine sediment core. Despite the fact that both marine sediment cores were retrieved from the tropics and cover the same glacial/interglacial periods, their mercury variations and the main drivers of mercury accumulations are dissimilar. Accordingly, we identified two different pathways by which mercury is incorporated into marine sediments for prolonged storage and inclusion in the global mercury biogeochemical cycle. The outcome of this study suggests that regional climate processes and geochemical conditions are essential to Hg variations in environmental archives. Another obvious finding is that the source of sedimentary organic carbon is a key determinant of their affinity for mercury.