Relative concentration of 13CH 4, 12CH 4 and 13CO 2, 12CO 2 in the atmosphere contains information about carbon dioxide and methane emission sources. High resolution of modern ground-based IR Fourier spectrometers allows one to resolve absorption lines of different isotopologues of the trace gases in atmospheric transmittance spectra. The modeling of synthetic atmospheric transmittance spectra within 2200–11000 cm -1 spectral region has been done and good signals of 13CH 4 and 13CO 2 were found. Several atmospheric transmittance spectra measured with ground-based FTIR at the Ural Atmospheric Station in Kourovka and at the Institute of Environmental Physics of Bremen University during 2010–2011 have been selected and processed. This paper presents a method and first results on the remote sensing of 13CH 4/ 12CH 4 (δ 13C CH4) and 13CO 2/ 12CO 2 (δ 13 CO2) in the atmoshpere.