Aircraft measurements of carbon and hydrogen isotopic ratios of atmospheric CH4 (δ13CH4 and δD-CH4), with the respective precisions of 0.08‰ and 2.2‰, as well as CH4 concentration were made at 1 and 2 km altitudes over western Siberia during 2006–2009. δ13CH4 and δD-CH4 were almost always lower at lower altitudes, while the CH4 concentration was higher, implying strong sources on the ground with low isotopic values. δ13CH4 showed a clear seasonal minimum in the late summer, while seasonality of CH4 and δD-CH4 was ambiguous due to the local disturbances. By inspecting the relationships between the CH4 concentration and isotopes, we found that isotopic source signatures in the winter (December–April) are −41.2 ± 1.8 and −187 ± 18‰ for δ13CH4 and δD-CH4, respectively, and the corresponding values in the summer (June–October) are −65.0 ± 2.5 and −282 ± 25‰. These values indicate predominant CH4emissions from fossil fuel facilities in the winter and wetlands in the summer. It was also found that the shorter-term CH4 variations are more influenced by fossil CH4 than that from wetlands. The finding presumably reflects the fact that the former is released from limited areas such as leakage from fossil fuel facilities, while the latter is released from a vast expanse of wetland. By employing a CH4 emission data set used in an atmospheric chemistry transport model, we calculated seasonal isotopic changes of CH4 sources in western Siberia and compared them to the estimates obtained in this study. The results indicated that the seasonal change in the CH4 emission data set is reasonable, at least in terms of a ratio of fossil to biogenic emissions.