In order to improve the understanding of structural and reactive features of sediment organic matter from mangrove swamp as well as evaluate the relationship between such features and the impact from different sources (marine and terrestrial), humic and fulvic acids were isolated from two mangrove swamp sediments located in the Qinglan harbors on Hainan Island, China. One is a forest surface sediment site (WWM2), and the other is an estuary subaqueous sediment site (BMW). The humic and fulvic acids were characterized and compared using chemical and spectroscopic methods, including elemental analysis, thermogravimetric analysis (TGA), Fourier Transformed Infrared Spectroscopy (FTIR), 13 C nuclear magnetic resonance ( 13 C NMR) and potentiometric titrations. The results indicated that there were less aliphatic compounds but more aromatic compounds and oxygen-containing functional groups in fulvic acids. Humic acids contained more long-chain hydrocarbons and nitrogen compounds. Comparison of the C/N ratios and δ 13 C values for the humic substances at both sites indicated a larger marine and/or microbial contribution to the BMW site. Humic substances at the WWM2 site have more acidic functional groups than those of the BMW site. Compared to the literature, more phenolic groups existed in the samples of both sites, which may be due to the autochthonous contribution of mangrove plants.