Permafrost peatlands are both an important source of atmospheric CH4 and a substantial sink for atmospheric CO2. Climate change can affect this balance, with higher temperatures resulting in the conversion of permafrost soils to wetlands and associated accelerated mineralisation and increased CH4 emission. To better understand the impact of such processes on methanogen populations, we investigated the anaerobic decay of soil carbon in a low Arctic, discontinuous permafrost peatland. Cores were collected monthly from sedge and Sphagnum mires in north Sweden during the summer of 2006. We determined CH4 concentrations and production potentials, together with variations in the size of the methanogenic community as indicated by concentrations of archaeal lipid biomarkers (phosphorylated archaeol, archaeol and hydroxyarchaeol). Concentrations of methanogen biomarkers generally were higher at the sedge site, increased with depth for all sites and months, and were usually below the detection limits in shallow (<10cm) Sphagnum peat. The distribution of biomarkers reflects the strong influence of water table depth on anaerobic conditions and methanogen populations, while differences in biomarker concentrations can be explained by differences in vegetation cover and pH. However, methanogen populations inferred from biomarker data show a decoupling from in-situ CH4 production over the season and from CH4 production potential, suggesting that other factors such as the availability of labile organic substrates can influence methanogen abundance. Archaeal lipid biomarkers appear to offer a potential new means to investigate permafrost biogeochemical processes but the interpretation of signals remains complex. Copyright (c) 2014 John Wiley & Sons, Ltd.