Boreal peatlands represent a considerable portion of the global carbon (C) pool. These environments are vulnerable to changes in water level (WL), which can vary dramatically in response to climate or land-use change. Water-level drawdown (WLD) causes peatland drying and induces a vegetation change, which in turn affects the decomposition of soil organic matter and the release of greenhouse gases (CO 2 and CH 4 ) into the atmosphere. The objective of this thesis was to study the microbial communities related to the C cycle and their response to WLD in two boreal peatlands.The first study site (Lakkasuo) is a boreal peatland complex that was partly drained in 1961 to investigate the long-term effects of WLD, and includes three site types with different nutrient levels. At the same location, an experiment simulating the predicted effect of climate change was carried out in 2001 to study the short-term effects of WLD. The second study site (Suonukkasuo) is a boreal fen with a WL gradient caused by a groundwater extraction plant; the undisturbed fen grades into a pine-dominated peatland forest. Microbial communities were studied with phospholipid fatty acid (PLFA) analysis, PCR-DGGE and multivariate analysis.Both sampling depth and site type had a strong impact on all microbial communities. In general, bacteria dominated the deeper layers of the nutrient-rich fen and the wettest surfaces of the nutrient-poor bog sites, whereas fungi seemed more abundant in the drier surfaces of the nutrient-poor bog. WLD clearly affected the microbial communities but the effect was dependent on site type. Fungi and Gram-negative bacteria seemed to benefit and actinobacteria to suffer from the WLD in the fens. The fungal and methane-oxidizing bacteria (MOB) community composition changed at all sites but the actinobacterial community response was apparent only in the nutrientrich fen after WLD.The actinobacterial response to WLD was minor compared to that of the fungal community. The response was greatest in the nutrient-rich fen and least in the nutrient-poor bog. Microbial communities became more similar among sites after long-term WLD. Litter quality had a large impact on community composition, whereas the effects of site type and WLD were relatively minor. The decomposition rate of fresh organic matter was influenced slightly by actinobacteria, but not at all by fungi. Overall, the results were in line with patterns of vegetation change in the study sites.Field respiration measurements in the northern fen indicated that short term WLD accelerates the decomposition of soil organic matter. In addition, a correlation between activity and certain fungal sequences indicated that community composition affects the decomposition of old organic matter in deeper layers of the peat profile. Fungal sequences were matched to taxa capable of utilizing a broad range of substrates. Most of the actinobacterial sequences could not be matched to characterized taxa in reference databases. WLD had a negative impact on CH 4 oxidation, especiall...