Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) was used to identify the qualitative differences between dissolved organic matter (DOM) in fen and bog porewaters from the Red Lake II system in the Glacial Lake Agassiz Peatlands (GLAP) of northern Minnesota. Approximately 80% of the molecular composition in surface porewater was maintained throughout the upper portion of the bog profile (0.17-2.50. m). The qualitative stability of the composition of the DOM was accompanied by a quantitative increase in dissolved organic carbon (DOC) with depth. The composition of DOM in the fen was significantly different at depth, with slightly varying DOC levels. Aromaticity index (AI) values were used to identify condensed aromatic and phenol-type compounds in the porewater of both peatlands. Surface bog and deep fen DOM had surprisingly similar molecular composition. Differences in enzymatic degradation rates via phenol oxidase in the bog and surface fen horizons, slower transport down the bog vertical profile and the presence of a stratum of Sphagnum-woody peat at depth in the fen are suggested as being responsible for the observed variations in DOM composition.