Sedimentary biomarker distributions can record ocean productivity and community structure, but their interpretation must consider alteration during organic matter (OM) export and burial. Large changes in the water column redox state are known to impact on the preservation of biomarkers, but more subtle variation in sediment redox conditions, characteristic of major modern ocean basins, have been less thoroughly investigated. Here we evaluate changes in biomarker distributions during sinking and burial across a nearshore to offshore transect in the southwestern Cape Basin (South East Atlantic), which includes a range of sedimentary environments. Biomarker concentrations and distributions in suspended particulate matter from the upper water column were determined and compared with underlying sedimentary biomarker accumulation rates and distributions. Biomarker distributions were similar in surface and subsurface waters, indicating that the OM signature is exported from the ocean mixed layer with minimal alteration. We show that, while export production (100 m) is similar along this transect, 230Thxs-corrected biomarker accumulation rate varies by over an order of magnitude in sediments and is directly associated with sedimentary redox conditions, ranging from oxic to nitrogenous–ferruginous. Biomarker distributions were dominated by sterols in surface water, and by alkenones in underlying sediments, which we propose to be primarily the result of selective preservation. Notably, the difference in sediment O2 penetration depth was associated with relative biomarker preservation. Subtle variation in sedimentary redox conditions has a dramatic impact on the distribution of preserved biomarkers. We discuss mechanisms for preferential degradation of specific biomarkers within this setting.