The eastern Mediterranean Sea sedimentary record is characterised by intervals of organic rich sediment (sapropels), indicating periods of severe anoxia triggered by astronomical forcing. It has been hypothesized that nitrogen fixation was crucial in injecting the Mediterranean Sea with bioavailable nitrogen (N) during sapropel events. However, the evolution of the N biogeochemical cycle of sapropels is poorly understood. For example, the role of the complementary removal reaction, anaerobic ammonium oxidation (anammox), has not been investigated because the traditional lipid biomarkers for anammox, ladderane fatty acids, are not stable over long periods in the sedimentary record. The recent development of an alternative lipid biomarker for anammox (bacteriohopanetetrol stereoisomer; BHT isomer) allowed for the investigation of anammox during sapropel deposition in this marginal sea. We present here the first application of a lipid biomarker for N removal throughout the progression (e.g. formation, propagation, and termination) of basin-wide anoxic events. In this study, BHT isomer and ladderanes were analysed in sapropel records taken from three Eastern Mediterranean sediment cores, spanning the most recent (S1) to Pliocene sapropels. Ladderanes were rapidly degraded in sediments, as recently as the S5 sapropel (ca. 125 ka). BHT isomer, however, was present in all sapropel sediments, as far back as the Pliocene (2.97 Ma), and clearly showed the response of anammox bacteria to marine water column redox shifts in high-resolution records. Two different N removal scenarios were observed in Mediterranean sapropels. During S5, anammox experienced Black Sea-like water column conditions, with the peak of BHT isomer coinciding with the core of the sapropel. Under the alternative scenario observed in the Pliocene sapropel, the anammox biomarker peaked at onset and termination of said sapropel, which may indicate sulphide inhibition of anammox during the core of sapropel deposition. This study shows the use of BHT isomer ...