This paper reports on the newly discovered occurrence of thick sequences (∼100 m) of Late Oligocene and Early Miocene (∼24.9 to ∼20 Ma) interbedded organic-rich sediments (sapropels) and pelagic (organic poor) carbonates at Sites U1466 and U1468 drilled in the Maldives archipelago during the International Ocean Discovery Program (IODP) Expedition 359. This occurrence is unusual in that this sequence is located > 1000 m above the surrounding ocean floor within an inter-atoll basin and not linked to any known global oceanic events. Total organic content reaches as high as 35% in the darker layers, while the interbedded carbonates have concentrations of less than 0.1%. Trace elements characteristic of anoxic waters, such as Mo, V, Cr, U, and Pb, correlate positively with concentrations of organic carbon. Nitrogen isotopic data show no evidence that the intervals of high total organic carbon are related to enhanced productivity driven by upwelling. Instead, high organic carbon is associated with intervals of anoxia. We propose that sea-level fluctuations linked to changes in Antarctic ice volume restricted exchange with the open ocean causing bottom waters of the inter-atoll basin to become anoxic periodically. The architecture of the platform at the end of the Oligocene, combined with the global sea-level highstand, set the stage for orbitally-driven sea-level changes producing cyclic deposition of sapropels. The proposed mechanism may serve as an analogue for other occurrences of organic carbon-rich sediments within carbonate platform settings.