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Bacteriohopanepolyols (BHPs), as a novel bacterial biomarker, show clear potential for tracking organic matter sources and environmental change. To evaluate BHPs as indicators of seasonal hypoxia in the Yangtze Estuary and its adjacent areas, the composition, distribution, and source of BHPs in surface sediments were analyzed using high-performance liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (HPLC-APCI-MS). A total of 12 BHPs were detected with a normalized TOC concentration of 3.79-269 μg·g -1 . The BHPs present in the surface sediments were dominated by bacteriohopanetetrol (BHT), 2-methyl-BHT, amino-BHPs, and adenosylhopane and its homologues, accounting for 40%, 22%, 12%, and 4% of the total BHPs, respectively. Each of these components and their corresponding indices show clear spatial trends. Specifically, BHT showed an "offshore increase" trend, which was mainly attributed to marine autochthonous inputs; and soil marker BHPs including adenosylhopane, which were dominated by terrestrial sources, showed an "offshore decrease" trend. The R soil index indicated a similar spatial pattern to the soil marker BHPs, with the relative contribution of terrestrial organic matter decreasing from 61.5% in coastal waters to 1.66% in the open ocean. This suggests that the organic matter in the coastal waters was mainly derived from terrestrial sources while marine sources were dominant in the open ocean. BHT-Ⅱ, the BHT stereoisomer, was derived from anaerobic ammonium oxidizing bacteria. High BHT-Ⅱ ratios were consistent with seasonal hypoxic zones in the Yangtze Estuary and, furthermore, these ratios were significantly negatively correlated with dissolved oxygen (DO) concentrations in the bottom waters. These observations indicate that hypoxic environments are beneficial to BHT-Ⅱ production, implying that BHT-Ⅱ can be used as an indicator of marine hypoxia.