Peatlands represent an important terrestrial pool of carbon, but are threatened by anthropogenic climate change, including a potential increase in drought events. Drought leads to the release of carbon dioxide from peat. It is well established that drought affects microbial communities, but so far insights into the microbial mechanisms underpinning the release of carbon from droughted peat are limited. In this project, temporally-explicit drought manipulations were carried out in two peatland habitats using a replicated and controlled series of mesocosm cores. ARISA fingerprinting was used to initially delimit shifts in microbial community composition, followed by shotgun metagenomic sequencing of a subset of samples and sequencing of SSU rRNA genes (marker gene analysis; MGA). DNA-based methodologies were accompanied by biogeochemical assays, which confirmed that drought conditions were achieved in treated cores relative to controls. ARISA fingerprinting demonstrated a significant effect of drought on bacterial and fungal community composition, with the most significant effect during the rewetting period. Conversely, sequencing-based methodologies detected a weak or non-existent effect of drought on overall community composition. However, MGA indicated that a subset of OTUs (operational taxonomic units) responded significantly to drought, particularly in the fen at 5cm depth. Where it was possible to assign taxonomy to drought-responsive OTUs, Proteobacteria and Bacteroidetes were overrepresented relative to their abundances in the community as a whole. In many cases, OTUs exhibiting negative responses to drought were closely related to obligate anaerobes. Rhizaria (a group of protists) also appeared to respond to drought. The abundance of hydA (a gene for the enzyme which catalyses the hydrogenic step in fermentation) fell during drought. To conclude, although the effect of drought on overall communities was weak, the analyses showed that a number of OTUs and functional genes responded to drought. The results provide numerous avenues for future research into the mechanisms underlying drought-driven carbon release from peatlands.