Abstract. The eastern Mediterranean Sea sedimentary record is characterised by intervals of organic-rich sapropel sediments, indicating periods of severe anoxia triggered by astronomical forcing. It has been hypothesised 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 reactions like 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. Using an alternative lipid biomarker for anammox, bacteriohopanetetrol stereoisomer (BHT isomer), we present here for the first time N removal throughout the progression, e.g. formation, propagation, and termination, of basin-wide anoxic events. BHT isomer and ladderanes were analysed in sapropel records taken from three eastern Mediterranean sediment cores, spanning S1 to Pliocene sapropels. Ladderanes were rapidly degraded in sediments, as recently as the S5 sapropel. BHT isomer, however, was present in all sapropel sediments, as far back as the Pliocene, 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-type 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 sulfide inhibition of anammox during the core of sapropel deposition. This study shows the use of BHT isomer as a biomarker for anammox in the marine sediment record and highlights its potential in reconstructing anammox during past anoxic events that are too old for ladderanes to be applied, e.g. the history of oxygen minimum zone expansion and oceanic anoxic events.