Coastal wetlands store significant amounts of carbon through sequestration. Salt marshes are also known to harbour high densities of crabs, which increase the sediment-atmosphere exchange interface through their burrowing behaviour. We hypothesized that this additional and reactive interface area could mediate gas exchange and, ultimately, could influence carbon sequestration. CO fluxes were measured over patches characterized by different densities of fiddler crab, , burrows within a natural salt marsh located on the coast of Massachusetts (USA). Even accounting for the importance of ecological factors such as differences in organic matter content of the soil and presence of , we demonstrated that CO release increased if local crab burrow density is considered. The increase in vertical CO fluxes linked to burrow density was higher for the non-vegetated areas with respect to patches. By means of burrow casting and morphological analyses of the burrows, we could relate this difference in COfluxes to structural differences of the burrows themselves, which were larger and deeper in the non-vegetated areas. Our results strongly emphasize the importance of including the faunal component, and specifically the dominant burrowing species, in carbon budget assessments for vegetated coastal habitats. This study also emphasizes the critical role of community-scale factors within the salt marsh, which are often overlooked, for large scale carbon budget assessments.