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Methanogens are methane-producing archaea (some of the most primitive organisms on Earth), which possess great phylogenetic and ecological diversity in modern ecosystems. However, cellular fossil evidence of methanogens remains extremely scarce throughout the geological record. Here, we report a new population of spheroidal microstructures composed of dolomite observed in Permian lake deposits in northwestern China. The microspheres exhibit indicators of biological affinity and are well preserved in authigenic dolomite with cellular fidelity. Based on morphological and geochemical evidence, these microspheres are interpreted as fossilized cells of methanogenic archaea, which can be divided into three size-based taxa. These microfossils are the first fossil record of spheroidal methanogens. The microfossil-bearing dolomite exhibits extremely positive δ13C values (up to +20‰ relative to Vienna Peedee belemnite) that are attributed to microbial methanogenesis. The results suggest that methanogens were a significant component of this Permian lake biosphere. As a consequence of the metabolic activity of the methanogens, a large amount of biogenic methane was produced through methanogenesis in the anoxic lake sediments. This study not only fills a gap in the fossil record of methanogenic archaea, but it also provides new insights into methane emissions from ancient lakes. [ABSTRACT FROM AUTHOR]