Species composition shifts in mangrove forests may alter organic matter dynamics. The purpose of this study was to predict the effect of species replacements among mangrove trees on organic matter dynamics in a mangrove forest on the island of Kosrae, Federated States of Micronesia. We were particularly interested in elements of the carbon cycle that affect peat accumulation rates, organic matter exports to the estuary and coral reef systems, and soil microbiology. We compared organic matter production and decomposition rates among three mangrove species that commonly grow in similar hydrogeomorphic settings: Rhizophora apiculata BL, which is selectively harvested; Bruguiera gymnorrhiza, which may gradually replace Rhizophora; and Sonneratia alba, which is producing few mature fruits. Sonneratia had significantly higher rates of root production (estimated with ingrowth chambers) than Bruguiera or Rhizophora. Sonneratia foliage had significantly faster decomposition rates and significantly lower lignin:nitrogen ratios than Bruguiera foliage. Live root mass was positively correlated with ingrowth and soil carbon, although soil carbon and ingrowth were not significantly correlated with each other. Humic acid concentrations were significantly higher in Sonneratia rhizospheres than in either Bruguiera or Rhizophora rhizospheres and were positively correlated with root ingrowth. The species changes taking place on Kosrae are likely to result in lower rates of root production and foliage decomposition, and more refractory carbon pools in soil.