An increased frequency of droughts due to anthropogenic climate change can lead to considerable stress for soil microorganisms and their functioning within northern peatlands. A better understanding of the diversity and abundance of methane producing and reducing taxa, and their functional genes, can help predict the functional potential of peatlands and how the microorganisms respond to disturbances such as drought. In order to address knowledge gaps in the understanding of how functional genetic diversity shifts under drought conditions, we investigated a hemi boreal mire in Southern Sweden. Environmental parameters, including soil and air temperature, precipitation and water table depth, as well as methane flux data were collected during the summer of 2017 under typical growing conditions, and in 2018 during a drought. In addition, the diversity and composition of genes encoding for methane metabolism were determined using the captured metagenomics technique. During drought we observed a substantial increase in air and soil temperature, reduced precipitation, and a lower water table depth. Taxonomic and functional gene composition significantly changed during the drought, while diversity indices, such as alpha and beta diversity, remained similar. These results indicate that methane producing and reducing microbial communities, and their functional genes, displayed a resilience to drought with specific genera having the ability to outcompete others under stress. Furthermore, our results show that although methane emissions are substantially reduced during drought, we can expect to see a shift towards more resilient methanogens and methanotrophs under future climate conditions.