Functional and structural aspects of the indigenous methanogenic and methanotrophic microbial populations were assessed in soil, peat and sediment from a hydroelectric reservoir (Robert-Bourassa) located in the subarctic Taiga. Three locations (un-flooded, seasonal flooding, and permanent flooding) in the reservoir were selected for sampling of forest soil and peat soil. Lakes located near the reservoir were also sampling for comparison with nearby unperturbed aquatic systems. Using samples incubated in microcosms at 5, 10 and 25°C, methane production and oxidation were quantified by gas chromatography. Structural aspects included bacterial counts of methanotrophic bacteria, and PCR amplification using 16S rDNA universal primers and primers specific for genes involved in methanogenesis or methanotrophy. Methanogenesis in the different systems appeared to depend on a combination of environmental factors, including the amounts and quality of organic carbon, and the abundance of oxidizing ions (Fe3+, SO4 2-). Periodically flooded or flooded peats contributed more to methane production than unflooded peats, soils and natural lake sediments. Similarly, methane oxidation rates were higher in peat soils than in flooded soils or lake sediments. The lowest rate of methane oxidation was observed in the forest soil, which was a typically undisturbed soil where the rate of CH4 production was close to the lower range of values observed in this study. This parallel evolution between the potential rate of methanogenesis and CH4 oxidation suggests an association between CH4 oxidation activity and CH4 supply. Methanogenesis appeared more sensitive to temperature increases than methanotrophy. The nucleotide sequences of PCR amplified and cloned mcrA fragment, a gene specific to methanogenesis revealed that many of the sequences obtained from the soils in this study were closely related to only uncultured clones of methanogens. Methanotrophic bacterial abundance was higher in flooded peat and lake sediment than in flooded soil, but abundance of methanotrophic bacteria in unflooded peat was lower than in unflooded forest soil. PCR amplification of genes specific to methanotrophic bacteria suggested that flooding of soil leads to a shift in populations of methanotrophic bacteria. A comparison of methane production and oxidation values obtained during this study indicated that essentially all of the methane produced in peat, forest soil and sediment could be oxidized within the system with little net atmospheric emission.