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Mangrove and salt marsh ecosystems are one of the most productive ecosystems in terrestrial systems, playing an important role in global carbon (C) cycling. The anaerobic condition in coastal wetland usually impedes the decomposition of soil organic carbon (SOC). However, the intrinsic stabilization mechanisms of SOC other than environmental factors are poorly understood in coastal wetland. In this paper, we investigated the relative contribution of mineral association and chemical compounds in maintaining the stabilization of SOC in the mangrove; salt marsh ecotone, and how the microbial community is involved in the stabilization. From NMR spectroscopy, we found that the SOC molecular structure of Sparffna. altemillora soils is simpler than that in mangrove forest, indicating an increased SOC decomposition with invasion of S. altemillora. On the contrary, the molecular structure of SOC in mangrove forest was dominated by recalcitrant aromatic C. Meanwhile, the larger fractions of silt/clay content in S. alterniflora and the transitional community were corresponding to higher percentage of mineral organic carbon (MOC), which suggest that the SOC in S. alterniflora vegetated soil was mainly protected by the mineral association. The transitional community contained highest MOC content probably due to both physical protection of mineral association and recalcitrant C input from adjacent mangroves. We also found that the fraction of SOC and its chemical structure of functional groups were associated with microbial communities. This study revealed the occurrence of different SOC stabilization mechanisms between mangroves and salt marshes. The knowledge gained may help to make predictions about future SOC dynamics as the different stabilization processes may response to climate change or human activities differently. (C) 2019 Elsevier B.V. All rights reserved.