We assessed the release of greenhouse gases (CO2 and CH4) from air-exposed sediments and dissolved inorganic carbon (DIC) from inundated sediments in 2 Brazilian mangrove forests. Our focus was on the impact of biogenic structures, i.e. pneumatophores and crab burrows, on greenhouse gas emissions. Emission of CO2 from air-exposed bare sediment (111-156 and 57-148 mmol m-2 d-1 in darkness and in light, respectively) was comparable to DIC release from inundated sediment (122-158 and 52-62 mmol m-2 d-1, respectively). Pneumatophores and crab burrows increased dark CO2 emission during air exposure by 113-123 and 49-91%, respectively. CH4 emission from air-exposed bare sediment (0.22-0.25 mmol m-2 d-1) was increased 92-137 and 288-607%, respectively, by pneumatophores and burrows. Carbon loss in the form of CO2 and DIC from sediments with biogenic structures can at the two study locations be extrapolated to 64.1 and 71.0 mol C m-2 yr-1. These values fit well with literature values of litterfall in the studied area, providing carbon accretion of 28.5 and 21.6 mol C m-2 yr-1. However, the budget will be unbalanced if the role of biogenic structures is not considered. In the presence of biogenic structures, CH4 emissions of 2.8 and 3.3 mol C m-2 yr-1 (when converted to CO2 units) will partly (10-15%) counteract the climate mitigation effect of the accumulated carbon. Carbon budgets in mangrove sediments may therefore be flawed if the contribution of biogenic structures to greenhouse gas emissions is ignored.