In Burkina Faso, African Animal Trypanosomosis (AAT) is still a major hindrance to cattle breeding, especially in the Mouhoun river basin, which was identified as a priority area for tsetse control. The abundance of tsetse flies and AAT risk were mapped using remote sensing coupled to field environmental data, along the Mouhoun river loop (more than 700 km long), where two tsetse species occur, Glossina palpalis gambiensis Vanderplank and G. tachinoides Westwood. The water course was classified into river sections of similar neighbouring where AAT risk was estimated using the entomological inoculation rate (EIR). Ten percent of the river course was sampled using biconical traps allowing measuring the relative densities of tsetse and their mature infection rates in the various landscapes which were used to estimate EIR distributions (@risk software). These results led to propose that the control of tsetse in this area should be focussed on the most dangerous sections.