The variability of methane flux with season, year, and habitat type was investigated in northern Minnesota peatlands from September 1988 through September 1990. Average daily fluxes calculated by integration of annual data for an open poor fen, an open bog, a forested bog hollow, a fen lagg in the forested bog and a forested bog hummock were 180,118, 38, 35, and 10 mg CH4m−2d−1, respectively. Fluxes among the five ecosystems were significantly different from one another, although emission from all sites was highest in July and lowest in March. Winter fluxes occurred in all sites but the fen lagg. There was no difference in fluxes measured from the same sites in the spring of 1986, 1989, or 1990, but summer fluxes were significantly higher in the wetter year of 1989 than in 1990, and a summer pulse in methane emission occurred in 1989 that was not seen the next year. Concentrations of methane in pore water, reflecting the seasonal balance of production, oxidation, and release, declined during the month of peak flux, then increased to levels of about 500 μM in December. Consistent spatial and temporal differences in flux could be ascribed to differences in water table, temperature, and peat nutrient status, although additional variability remained. Integration gave an annual average flux of 20 g CH4, m−2ot; for the three bog ecosystems and 39 g CH4, m−2for the two fen ecosystems. This gives an estimate of 1–2 Tg CH4, yr−1from peatlands in the Great Lake states of Minnesota, Wisconsin,