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Understanding the interaction between molybdenum (Mo) and organic matter during microbial sulfate reduction is critical for the use of Mo to reconstruct marine redox conditions throughout Earth's history. However, little is known about Mo isotope fractionation and how it relates to organic matter remineralization during microbial sulfate reduction. Here, we report Mo abundances and isotopic (δ98Mo) compositions for bulk‐rock, non‐lithogenic and sequentially extracted fractions, including carbonate (carb), pyrite, and organic matter (OM), of seep carbonate rocks. Our data indicate that the difference between δ98Mocarb and δ98MoOM (Δ98Mocarb‐OM) displays significant variability in the studied samples, ranging between 0.72 and 1.01‰. Remarkably, the obtained Δ98Mocarb‐OM values indicate correlative trends with stable carbon isotope ratios and bulk abundances of (a) total organic carbon, (b) Mo, and (c) pyrite in seep carbonates, which we interpret as reflecting sustained adsorption of isotopically light Mo onto organic matter during enhanced sulfate reduction. On this basis, we put forward the concept that Δ98Mocarb‐OM of authigenic carbonate rocks can be used as a measure of the intensity of sulfate reduction and for reconstructing past interactions between Mo and organic matter in marine sediments. Plain Language Summary: Molybdenum (Mo) is a useful element for reconstructing marine redox conditions throughout the Earth's history. The sequestration of Mo through sulfate‐reducing bacterial activity acts as a significant pathway for Mo burial in the ocean. However, the impact of microbial sulfate reduction in Mo isotope fractionation remains unclear, preventing the understanding of the interaction between Mo and organic matter. We report Mo abundances and isotopic (δ98Mo) compositions for different phases extracted from seep carbonate rock fractions, including carbonate (carb), pyrite, and organic matter (OM). Our findings indicate that organic matter tends to preferentially adsorb isotopically light Mo. The observed δ98Mo difference between carbonate and organic matter fractions (Δ98Mocarb‐OM from 0.72 to 1.01‰) represents the first report of the extent of Mo isotope fractionation during Mo adsorption to organic matter in marine environments. We attribute greater Δ98Mocarb‐OM offsets to the preferential adsorption of isotopically light Mo onto organic matter during enhanced sulfate reduction, and in turn put forward the idea that such offsets can be possibly used in the sedimentary record to trace the intensity of sulfate reduction and to reconstruct the past interaction between Mo and organic matter in marine sediments. Key Points: Organic matter tends to adsorb isotopically light Mo, resulting in low δ98Mo values of organic matter in marine environmentsIsotopically light Mo is inferred to be preferentially adsorbed onto organic matter during enhanced sulfate reductionδ98Mo offset between carbonate and organic phases in authigenic carbonates is promising to trace the past intensity of sulfate reduction [ABSTRACT FROM AUTHOR]