Permafrost soils are critical reservoirs for mercury (Hg), with the thawing process leading to the release of this element into the environment, posing significant environmental risks. Of particular concern is the methylated form of mercury, monomethylmercury (MMHg), known for its adverse effects on Human health. Microbial communities play a pivotal role in the formation of MMHg by facilitating Hg methylation, yet the specific types of microbes involved still need to be understood. Microorganisms play also a role in the demethylation of MMHg, slowing the crossing of toxic threshold concentration in the environment. This study aimed to identify the microbial drivers behind changes in Hg speciation (MMHg and Hg) in permafrost thaw lakes and assess the significance of the biotic component in Hg biogeochemistry. Sediment samples were collected from two thermokarst lakes in the Canadian sub-arctic throughout the Winter and Summer of 2022. Gene-centric metagenomic applied on whole genome sequencing (WGS) was conducted to identify the genes involved in Hg methylation (hgcA and hgcB) and demethylation (merA and merB), and hgcA and hgcB confirmed by qPCR. The microbial communities showed to be involved in the Hg cycle shifted coherently with the MMHg and total Hg measurements. Particularly, the diversity of this group of prokaryotes decreased from winter to summer. HgcA, merA, and merB coverage were low in summer, while they drastically increased during winter, similarly in all soil depth layers investigated, consistently with the MMHg levels measured. Notably, MMHg values in winter were two to five times higher than measured in summer. Our study provides new insights in the microbial contribution to the Hg cycle in the Arctic degrading permafrost.