Shrub/Tree and sedge/grass peatlands cover millions of hectares throughout the South Atlantic coast (SAC) that range from the Great Dismal Swamp in VA, through North Carolina, into the lower Atlantic coastal plain, the Okefenokee Swamp in Georgia, to the Cladium dominated Florida Everglades. These peatlands store about 1/5 of soil carbon in peatlands in the USA (not including Alaska). There are substantial scientific gaps required to manage these ecosystems in the face of global climate changes and drainage for agriculture or forestry. Here we explore the mechanisms that control peat decomposition and have enabled these ancient SAC mires to build and maintain peat in the face of long-term patterns of climate driven increases in recurring oxidative disturbances as well as anthropogenic drainage. Our data shows that the long-term stability of SAC peat stems from inputs of decay resistant plant litter (high-phenol content /low carbon quality) and by fire adapted evergreen shrub/tree or Cladium communities. Our early results indicate peat carbon quality is regulated by three environmental factors. Phenolics, black carbon and lignin complexes, which are the core chemical control on decomposition is regulated by biotic and abiotic factors—species, hydrology and fire. We present a dual control model that describes the feedback mechanisms regulating carbon storage and losses in these coastal peatlands under drought or drainage effects. An example of the amount of carbon retained that otherwise would be lost without restoration (stop loss), the amount retained in peat as soil genesis is re-established, and the amount retained in the above ground biomass indicates that total carbon stored by restoration could reach nearly 7,300 kg/ha/yr in one peatland complex in North Carolina. The approach used in this study provides the basis for development of a soil carbon protocol that could be established for the promising U.S. carbon credit market.