The space-time variations of the carbon budget at the Earth's surface are highly variable and quantifying them represents a major scientific challenge. One strategy consists in inferring the carbon surface fluxes from the atmospheric concentrations. An inversion scheme for the hydrocarbon oxidation chain, that includes CO and CH4, is presented here with a focus on the African continent. It is based on a variational principle. The multi-tracer system has been built as an extension of a system initially developed for CO2 and includes a new simplified non-linear chemistry module. Individual in situ measurements of methyl-chloroform and individual retrievals of CO concentrations from the Measurements Of Pollution In The Troposphere (MOPITT) space-born instrument have been processed by the new system for the period 2000-2006 to infer the time series of CO emissions at the resolution of 2.5°×3.75° (latitude, longitude). It is shown that the analysed concentrations improve the fit to five independent surface measurement stations located in or near Africa by up to 28% compared to standard inventories, which confirms that significant information about CO emissions can be obtained from MOPITT data. In practice, the inversion reduces the amplitude and the interannual variability of the seasonal cycle in the northern part of Africa, with a longer burning season. In the southern part, the inversion mainly shifts the emission peak by one month later in the season, consistent with previously-published inversion results.