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Background  Genetic variation of microsatellite loci is a widely used method for the analysis of population genetic structure of several organisms. To improve our knowledge on the population genetics of trypanosomes,  Trypanosoma congolense  forest and savannah types were identified in the mid-guts of  Glossina palpalis palpalis  caught in five villages of Fontem in the South-West region of Cameroon. From the positive samples of  Trypanosoma congolense  forest, the genetic diversity and the population genetic structure of these parasites were evaluated.    Method  For this study, pyramidal traps were set up during three entomological surveys and 3347 tsetse flies were collected, dissected and 1903 midguts collected. DNA was extracted from midguts and specific primers were used to identify  Trypanosoma congolense  forest and savannah. All  Trypanosoma congolense  forest positive samples were characterized with seven microsatellite markers.    Results  Microscopic examination revealed 25 (1.31%) mid-gut infections with trypanosomes while the PCR method identified 120 (6.3%) infections due to  Trypanosoma congolense:  94 (78.33%)  Trypanosoma congolense  forest and 28 (21.77%)  Trypanosoma congolense  savannah. The trypanosome infection rates varied significantly between villages and years of capture. Menji recorded the highest infection rate (15.11%); and samples captured in 2009 were more infected (14.33%). The microsatellite markers revealed a genetic variability between  Trypanosoma congolense  forest populations of Fontem villages and 6.38% of mixed infections due to different genotypes of  T. congolense  “forest type”.    Conclusion  Our data on the population genetics play in favor of a clonal reproduction of this parasite. The microsatellite markers used here showed a low genetic differentiation and an absence of sub-structuration ( F  ST  ≤ 0.0003) between  Trypanosoma congolense  forest populations of Fontem villages. However, the high  F  ST  value ( F  ST  ≥ 0.3911) between samples of the Democratic Republic of Congo and those of Fontem villages indicates low migration rates between trypanosomes of these subpopulations.    Electronic supplementary material  The online version of this article (doi:10.1186/1756-3305-7-385) contains supplementary material, which is available to authorized users.

Population genetics of forest type of Trypanosoma congolense circulating in Glossina palpalis palpalis of Fontem in the South-West region of Cameroon