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Summary Marine microorganisms play a fundamental role in the global carbon cycle by mediating the sequestration of organic matter in ocean waters and sediments. A better understanding of how biological factors, such as microbial community composition, influence the lability and fate of organic matter is needed. Here, we explored the extent to which organic matter remineralization is influenced by species‐specific metabolic capabilities. We carried out aerobic time‐series incubations of Guaymas Basin sediments to quantify the dynamics of carbon utilization by two different heterotrophic marine isolates (Vibrio splendidus1A01;Pseudoalteromonassp. 3D05). Continuous measurement of respiratory CO₂production and its carbon isotopic compositions (¹³C and¹⁴C) shows species‐specific differences in the rate, quantity and type of organic matter remineralized. Each species was incubated with hydrothermally‐influenced versus unimpacted sediments, resulting in a ~2‐fold difference in respiratory CO₂yield across the experiments. Genomic analysis indicated that the observed carbon utilization patterns may be attributed in part to the number of gene copies encoding for extracellular hydrolytic enzymes. Our results demonstrate that the lability and remineralization of organic matter in marine environments is not only a function of chemical composition and/or environmental conditions, but also a function of the microorganisms that are present and active.