The role of environmental factors in driving adaptive trajectories of living organisms is still being debated. This is even more important to understand when dealing with important and /or neglected diseases and their vectors. In this paper, we analysed genetic divergence, computed from several genetic markers, of 614 tsetse flies (Glossina palpalis gambiensis and Glossina palpalis palpalis, major vectors of animal and human trypanosomes) from 28 sites of West and Central Africa. We found that the two subspecies are so divergent that they deserve the species status. We found that G. p. gambiensis from different landscapes (Niayes of Senegal, savannah and coastal environments) were significantly genetically different, and thus represent different adaptive entities or even subspecies. We also confirm that G. p. palpalis from Ivory Coast, Cameroon and DRC are strongly divergent. These results provide an opportunity to examine whether these different types of tsetse fly might display different behaviour, dispersal patterns, host preferences and vectorial capacities. This work also urges a revision of taxonomic status of Glossina palpalis subspecies and highlights again how fast ecological divergence can be, especially in hostparasite- vector systems.