In Burkina Faso, the Mouhoun river basin (formerly "Black Volta") constitutes a historical focus of Human (HAT) and Animal (AAT) African Trypanosomoses, both transmitted by tsetse flies. Nowadays, HAT seems to have disappeared from this area, while AAT still causes severe economic losses. In order to explain these different epidemiological situations, we undertook a geographical study based on the analysis of aerial pictures between 1952 and 2007, and field surveys to collect medical, entomological, and veterinary data on trypanosomoses. Our results suggest that in this area, landscapes have been dramatically modified as a consequence of population growth, and in turn have had an impact on the number and distribution of tsetse flies. Combined with the historical medical action on HAT which probably led to the disappearance of T. b. gambiense, this environmental degradation and the development of hydrological structures provide explanations for the local disappearance of HAT, and for the maintenance of AAT. It appears necessary to extrapolate these studies to other areas in order to identify the factors explaining the presence/absence of trypanosomoses in the context of human population growth and climatic changes, in order to help to target priority areas for the control of these diseases.