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Mangroves store a large amount of organic carbon (OC) within the sediment to a depth of a meter or beyond. Nevertheless, little information is available about the difference in chemical composition of sedimentary OC in young restored versus old intact forests. To understand such pattern of changes in molecular composition of OC according to mangrove development, we conducted a detailed study at two contrasting settings on the Panay Island, the Philippines, where sediment properties were examined by applying advanced measurement tools (e.g.1H nuclear magnetic resonance spectroscopy and C and N stable isotopes), in addition to biomass and water quality data. Organic carbon was preserved in greater proportion with mangrove development (6 months to 40 years old) as indicated by its higher ratio to specific surface area (OC/SSA, 61 to 143 μmol C m 2) and stock estimates (from young to old as above-ground biomass: 27 to 568 Mg dry matter ha 1, below-ground biomass: 14 to 309 Mg dry matter ha 1, sediment: 28 to 77 Mg C ha 1 between 0 cm and 50 cm depth). Chemical differences between alkali-extractable OC samples were visible in the chemical shift regions of 1H NMR, as we found a distinct separation of sediment from the old to the young sites. The relative abundances of the % olefinic H and % carbohydrate H were higher in the sediment of old mature stands than the young, restored sites, where % aliphatic H and % functionalized aliphatic H dominated. The composition of alkali-extractable OC was determined mainly by the forest age, sediment depth and decomposition of mangrove-derived OC input. Finally, this work provides important baseline information for future projection of sediment maturity level after plantation in the studied mangrove forest.