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Coastal ecosystems can efficiently remove carbon dioxide (CO 2 ) from the atmosphere and are thus promoted for nature-based climate change mitigation. Natural methane (CH 4 ) emissions from these ecosystems may counterbalance atmospheric CO 2 uptake. Still, knowledge of mechanisms sustaining such CH 4 emissions and their contribution to net radiative forcing remains scarce for globally prevalent macroalgae, mixed vegetation, and surrounding depositional sediment habitats. Here we show that these habitats emit CH 4 in the range of 0.1 - 2.9 mg CH 4  m -2  d -1 to the atmosphere, revealing in situ CH 4 emissions from macroalgae that were sustained by divergent methanogenic archaea in anoxic microsites. Over an annual cycle, CO 2 -equivalent CH 4 emissions offset 28 and 35% of the carbon sink capacity attributed to atmospheric CO 2 uptake in the macroalgae and mixed vegetation habitats, respectively, and augment net CO 2 release of unvegetated sediments by 57%. Accounting for CH 4 alongside CO 2 sea-air fluxes and identifying the mechanisms controlling these emissions is crucial to constrain the potential of coastal ecosystems as net atmospheric carbon sinks and develop informed climate mitigation strategies., (© 2023. The Author(s).)