Carbon dioxide (CO<sub>2</sub>) and methane (CH<sub>4</sub>) are the two most important anthropogenic greenhouse gases contributing to global climate change. SCIAMACHY onboard ENVISAT (launch 2002) was the first and is now with TANSO onboard GOSAT (launch 2009) one of only two satellite instruments currently in space whose measurements are sensitive to CO<sub>2</sub> and CH<sub>4</sub> concentration changes in the lowest atmospheric layers where the variability due to sources and sinks is largest. <br><br> We present long-term SCIAMACHY retrievals (2003–2009) of column-averaged dry air mole fractions of both gases (denoted XCO<sub>2</sub> and XCH<sub>4</sub>) derived from absorption bands in the near-infrared/shortwave-infrared (NIR/SWIR) spectral region focusing on large-scale features. The results are obtained using an upgraded version (v2) of the retrieval algorithm WFM-DOAS including several improvements, while simultaneously maintaining its high processing speed. The retrieved mole fractions are compared to global model simulations (CarbonTracker XCO<sub>2</sub> and TM5 XCH<sub>4</sub>) being optimised by assimilating highly accurate surface measurements from the NOAA/ESRL network and taking the SCIAMACHY averaging kernels into account. The comparisons address seasonal variations and long-term characteristics. <br><br> The steady increase of atmospheric carbon dioxide primarily caused by the burning of fossil fuels can be clearly observed with SCIAMACHY globally. The retrieved global annual mean XCO<sub>2</sub> increase agrees with CarbonTracker within the error bars (1.80±0.13 ppm yr<sup>−1</sup> compared to 1.81±0.09 ppm yr<sup>−1</sup>). The amplitude of the XCO<sub>2</sub> seasonal cycle as retrieved by SCIAMACHY, which is 4.3±0.2 ppm for the Northern Hemisphere and 1.4±0.2 ppm for the Southern Hemisphere, is on average about 1 ppm larger than for CarbonTracker. <br><br> An investigation of the boreal forest carbon uptake during the growing season via the analysis of longitudinal gradients shows good agreement between SCIAMACHY and CarbonTracker concerning the overall magnitude of the gradients and their annual variations. The analysis includes a discussion of the relative uptake strengths of the Russian and North American boreal forest regions. <br><br> The retrieved XCH<sub>4</sub> results show that after years of stability, atmospheric methane has started to rise again in recent years which is consistent with surface measurements. The largest increase is observed for the tropics and northern mid- and high-latitudes amounting to about 7.5±1.5 ppb yr<sup>−1</sup> since 2007. Due care has been exercised to minimise the influence of detector degradation on the quantitative estimate of this anomaly.