AbstractThe thawing and subsidence of frozen peat mounds (palsas) in permafrost landscapes results in the formation of organic‐rich thermokarst lakes. We examined the effects of palsa degradation on CH4 and CO2 emissions by comparing thermokarst lakes at two peatland locations in subarctic Québec, Canada: in the northern discontinuous permafrost region, and in southern sporadic permafrost where palsas are more rapidly degrading. The lakes were shallow (< 3 m) but stratified at both sites, and most had anoxic bottom waters. The surface waters at both sites were supersaturated in CH4 and CO2, and to a greater extent in the southern lakes, where the surface CH4 concentrations were up to 3 orders of magnitude above air equilibrium. Concentrations of CH4 and CO2 increased by orders of magnitude with depth in the southern lakes, however these gradients were less marked or absent in the North. Strong CH4 and CO2 emissions were associated with gas ebullition, but these were greatly exceeded by diffusive fluxes, in contrast to thermokarst lakes studied elsewhere. Also unusual relative to other studies to date, the surface concentrations of both gases increased as a linear function of water column depth, with highest values over the central, deepest portion of the lakes. Radiocarbon dating of ebullition gas samples showed that the CH4 had 14C‐ages from 760 yr to 2005 yr before present, while the CO2 was consistently younger. Peatland thermokarst lakes may be an increasingly important source of greenhouse gases as the southern permafrost limit continues to shift northwards.