Bogs and fens from northern Minnesota produce large quantities of CH4, which may be either emitted to the atmosphere or stored in below-ground reservoirs. The identity of the organic materials that support CH4 production has been uncertain, but we present evidence that a significant fraction of surface emission and below-ground CH4 is derived from recently fixed organic compounds. First, the CH4 emitted from both bogs and fens has a '4C signature equivalent to contemporary values for atmospheric CO2. Second, in flooded fens rates of CH4 emission are linearly related to rates of CO2 exchange and to the δ13C of emitted CH4. Third, peat-porewaters as deep as several meters below the surface contain mixtures of CH4 derived from both modern and older organic substrates. The source of the modern organic substrates is most likely dissolved organic compounds produced from the decay of recently produced litter, roots and root exudation products and transported into deeper layers of the peat. These data indicate that CH4 emissions are closely linked to the living vegetation and hydrology of northern peatlands and less dependent on the lability and decomposition of peat within the deeper layers of the catotelm.