The impact of landscape fragmentation resulting from human- and climate-mediated factors on the structure of a population of Glossina tachinoides Westwood (Diptera: Glossinidae) in the Mouhoun River basin, Burkina Faso, was investigated. Allele frequencies at five microsatellite loci were compared in four populations. The average distance between samples was 72 km. The sampling points traversed an ecological cline in terms of rainfall and riverine forest ecotype, along a river loop that enlarged from upstream to downstream. Microsatellite DNA demonstrated no structuring among the groups studied (F(ST) = 0.015, P = 0.07), which is contrary to findings pertaining to Glossina palpalis gambiensis Vanderplank in the same geographical area. The populations of G. tachinoides showed complete panmixia (F(IS) = 0, P = 0.5 for the whole sample) and no genetic differentiation among populations or global positioning system trap locations. This is in line with the results of dispersal studies which indicated higher diffusion coefficients for G. tachinoides than for G. p. gambiensis. The impact of these findings is discussed within the framework of control campaigns currently promoted by the Pan African Tsetse and Trypanosomosis Eradication Campaign.