The Great Dismal Swamp (GDS) is a large temperate swamp in Virginia/North Carolina with peat soils historically resistant to microbial decomposition. However, this peatland has been subject to ~200 years of disturbance during which extensive drainage, fire suppression, and wide-spread logging have increased decomposition and dramatically decreased the distribution of Atlantic white cedar (AWC). The purpose of this study was to determine the impact of long-term drainage and AWC loss on the carbon chemistry of GDS peats. Peat cores were collected from three drained GDS vegetation communities (pocosin, AWC, and red maple-black gum) and compared to cores collected from an intact, undrained AWC peatland at the Alligator River National Wildlife Refuge (AR) in North Carolina, USA. The AR peats had higher lignin content in the deeper peat intervals, and lignin content and % organic carbon were largely invariant with depth compared to the GDS peats. The concentrations of syringyl group phenols were greater in the surface layers of GDS peats, likely reflecting the selective removal of AWC and transition from gymnosperms to angiosperms. Acid to aldehyde ratios for vanillyl and syringyl group phenols indicated that the GDS peats were more decomposed, particularly at depth, and that this occurred under aerobic conditions. Moreover, solid state 13C NMR confirmed a coincident loss of carbohydrates and increase in recalcitrant byproducts of carbohydrate degradation with depth. These data indicate that long-term drainage has accelerated the decomposition of peat at the GDS, reducing the capacity and stability of the carbon sink.