Northern latitude peatlands act as important carbon sources and sinks but little is known about the greenhouse 30 gas (GHG) budget of peatlands submerged beneath the North Sea during the last glacial-interglacial transition. We found that whilst peat formation was diachronous, commencing between 13,680 and 8,360 calibrated years before the present, stratigraphic layering and local vegetation succession were consistent across a large study area. The CH4 concentrations of the sediment pore waters were low at most sites, with the exception of two 35 locations, and the stored carbon was large. Incubation experiments in the laboratory revealed molecular signatures of methanogenic archaea, with strong increases in rates of activity upon methylated substrate amendment. Remarkably, methanotrophic activity and the respective diagnostic molecular signatures could be not be detected. Heterotrophic Bathyarchaeia dominated the 40 archaeal communities and bacterial populations were dominated by candidate phylum JS1 bacteria. Although CH4 accumulation is low at most sites, the presence of in situ methanogenic micro-organisms, the absence of methanotrophy, and large widespread stores of carbon hold the potential for GHG production if catalysed by a change in environmental conditions. Despite being earmarked as a critical source of CH4 seepage, 45 seepage from these basal-peat deposits is restricted, as evidenced by low in situ CH4 concentrations.