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Models predict that thaw of permafrost soils at northern high latitudes will release tens of billions of tonnes of carbon (C) to the atmosphere by 2100 (refs 1-3). The effect on the Earth's climate depends strongly on the proportion of this C that is released as the more powerful greenhouse gas methane (CH4), rather than carbon dioxide (CO2) (refs 1,4); even if CH4 emissions represent just 2% of the C release, they would contribute approximately one-quarter of the climate forcing(5). In northern peatlands, thaw of ice-rich permafrost causes surface subsidence (thermokarst) and water-logging(6), exposing substantial stores (tens of kilograms of C per square meter, ref. 7) of previously frozen organic matter to anaerobic conditions, and generating ideal conditions for permafrost-derived CH4 release. Here we show that, contrary to expectations, although substantial CH4 fluxes (>20 g CH4 m(-2) yr(-1)) were recorded from thawing peatlands in northern Canada, only a small amount was derived from previously frozen C (<2 g CH4 m(-2) yr(-1)). Instead, fluxes were driven by anaerobic decomposition of recentCinputs. We conclude that thaw-induced changes in surface wetness and wetland area, rather than the anaerobic decomposition of previously frozen C, may determine the effect of permafrost thaw on CH4 emissions from northern peatlands.