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Blue carbon is the organic carbon in oceanic and coastal ecosystems that is captured on centennial to millennial timescales. Maintaining and increasing blue carbon is an integral component of strategies to mitigate global warming. Marine vegetated ecosystems (especially seagrass meadows, mangrove forests, and tidal marshes) are blue carbon hotspots as organic carbon is buried within their habitat and in surrounding environments. In addition, depositional environments throughout the ocean can also provide an important global sink of blue carbon, including carbon from macroalgae and other primary producers. Tracking the source and fate of organic carbon throughout oceans will support conservation and restoration schemes aimed at enhancing blue carbon sequestration and avoiding greenhouse gas emissions. Here we review recent research and the potential of genomic based techniques to track the provenance and fate of organic carbon and highlight next-steps in validating the use of eDNA to track and even quantify the sources of organic carbon in marine environments.