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Using an atmospheric inversion approach, we estimate methane surface emissions for different methane regional sources between 1996 and 2001. Data from 13 high-frequency and 79 low-frequency CH4 observing sites have been averaged into monthly mean values with associated errors arising from instrumental precision, mismatch error, and sampling frequency. Simulated methane mole fractions are generated using the 3-D global chemical transport model (MATCH), driven by NCEP analyzed observed meteorology (T62 resolution), which accounts for the impact of synoptic and interannually varying transport on methane observations. We adapted the Kalman filter to optimally estimate methane flux magnitudes and uncertainties from seven seasonally varying (monthly varying flux) and two aseasonal sources (constant flux). We further tested the sensitivity of the inversion to different observing sites, filtered versus unfiltered observations, different model sampling strategies, and alternative emitting regions. Over the 1996–2001 period the inversion reduces energy emissions and increases rice and biomass burning emissions relative to the a priori emissions. The global seasonal emission peak is shifted from August to July because of increased rice and wetland emissions from southeast Asia. The inversion also attributes the large 1998 increase in atmospheric CH4 to global wetland emissions. The current CH4 observational network can significantly constrain northern emitting regions but not tropical emitting regions. Better estimates of global OH fluctuations are also necessary to fully describe interannual methane observations. This is evident in the inability of the optimized emissions to fully reproduce the observations at Samoa.