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Using ancient environmental DNA (eDNA) we reconstructed microbial and viral communities from the Kap København Formation in North Greenland. We find pioneer microbial communities, along with likely dormant methanogens from the permafrost’s seed bank. Our findings reveal that at the time of the formation, the terrestrial input of the Kap København site originated from a palustrine wetland, suggesting non-permafrost conditions. During this time, detection of methanogenic archaea and carbon processing pathways suggests a moderate strengthening of methane emissions through the northward expansion of wetlands. Intriguingly, we discover a remarkable sequence similarity (>98%) between pioneer methanogens and present-day thawing permafrost counterparts. This suggests that not all microbes respond uniformly to environmental change over geological timescales, but that some microbial taxa’s adaptability and resilience remain constant over time. Our findings further suggest that the composition of microbial communities is changing prior to plant communities as a result of global warming.