The abundance and structural diversity of bacteriohopanepolyols (BHPs) was examined in three marine pelagic environments that are characterized by strong vertical redox gradients and water column suboxia or anoxia. The abundance and, in most instances, structural diversity of BHPs was highest at depths where conditions were suboxic or anoxic. However, the majority of the BHP structures that were identified are environmentally cosmopolitan and their biological sources are presently not well constrained. An isomer of bacteriohopanetetrol (denoted BHT II) was observed at all three study sites in association with anoxic and suboxic conditions within the water column. Based on the absence of BHT II from terrigenous and oxic marine environments studied to date, and its strong association with suboxic and anoxic marine pelagic environments, we propose that BHT II is a promising candidate biomarker for water column suboxia and anoxia in the marine geologic record. The molecular fingerprint of BHPs in suspended and sinking particles and core-top sediments indicates that hopanoids produced within the water column are exported to marine sediments and that their biological source is most likely associated with settling particles and not the free-water phase. Based on our observations, BHPs likely represent an important input to the sedimentary hopanoid inventory, particularly in upwelling environments characterized by pelagic oxygen minimum zones (OMZ) and anoxic marine basins.