The chemical structure of refractory marine dissolved organic matter (DOM) is still largely unknown. Electrospray Ionisation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (ESI FT-ICR-MS) resolved the complex mixtures of DOM and provided valuable information on elemental compositions on a molecular scale. We characterised and compared DOM from two sharply contrasting aquatic environments, algal-derived DOM from the Weddell Sea (Antarctica) and terrigenous DOM from seawater of a tropical mangrove area in northern Brazil. Several thousand molecular formulas in the mass range of 300-600 Da were identified and reproduced in element ratio plots. On the basis of molecular elemental composition and double bond equivalents (DBE) we calculated an average composition for marine DOM. O/C ratios in the marine samples were lower (0.36 ± 0.01) than in the mangrove porewater sample (0.42). A small proportion of chemical formulas with higher molecular mass in the marine samples were characterised by very low O/C and H/C ratios probably reflecting amphiphilic properties. The average number of unsaturations in the marine samples was surprisingly high (DBE = 9.9; mangrove porewater: DBE = 9.4) most likely due to a significant contribution of carbonyl carbon. Apart from higher DBE in the deep-water samples there was no significant difference between surface and deep-water in the Weddell Sea. Although there were some molecules with unique marine elemental composition, there was a conspicuous degree of similarity between the terrigenous and algal-derived endmembers. Approximately one third of the molecular formulas were present in all marine as well as in the mangrove samples. We infer that the most different forms of microbial degradation in the biosphere ultimately lead to similar structural features that are intrinsically refractory, independent of the ultimate source of organic matter and the environmental conditions where degradation took place.