Mangrove deforestation threatens to release large stores of carbon from soils that are vulnerable to oxidation. Carbon stored in deep soils is not measured in national carbon inventories. Thus, policies on emission reductions have likely underestimated the contribution of mangrove deforestation to national emissions. Here, we estimate that emissions from deforestation and degradation of mangroves in Mexico are 31 times greater than the values used to determine national emission reduction targets for the Paris Agreement. Thus, Mexico has vastly undervaluated the potential of mangrove protection to reduce its emissions. Accounting for carbon emissions from mangrove soils should greatly increase the priority of mangrove forests to receive funding for protection under carbon trading programs.