Oceanic anoxic events (OAE) in the Cretaceous represent major perturbations in the global climate and ocean system characterized by widespread deposition of organic carbon in the ocean. The causes and effects of these events are poorly constrained, mainly because of the lack of high-resolution marine records. Here we report the distribution of molecular markers from a millennial-scale record of Coniacian-Santonian black shale (OAE-3) from Ocean Drilling Program Site 959 in the Deep Ivorian Basin in the eastern equatorial Atlantic. Highly branched isoprenoids and alkenone-derived organic compounds indicate that diatoms and calcareous nanoplankton were important primary producers. Changes in redox sensitive trace metal accumulation and biomarkers of green sulfur bacteria provide evidence for extreme variations in redox conditions, with intervals of lower photic zone euxinia (PZE). Accordingly, oxygen in the Coniacian-Santonian tropical Atlantic was absent as during the Cenomanian-Turonian boundary OAE-2 but over more restricted geographic area and more limited time intervals. We hypothesize that PZE was a common phenomenon typical in large areas of tropical continental margins. These conditions fostered sequestration of atmospheric CO2 and thus helped cause the positive excursion in δ13C of carbonate documented in higher latitude marine records.