This manuscript (word file), presents results obtained while developing microsatellite markers for the parasite T. lewisi and the first population genetics data analysis for this species. This parasite is found mainly in rodents (rats) and is transmitted by fleas. To this respect, it shares the same cycle as other human pathogens (plague, murine typhus) The first results suggest that the subpopulation unit for these parasite populations may be found at very small scales, neighborhoods of cities, and probably even at lower scales (e.g. homes). Data also suggest an operational life cycle (generation time) of 1-2 months, as for other trypanosome species. The excel file contains all raw data and primer sequences. This paper was evaluated through Peer Community In Infectious Diseases and this is the new version after taking into account Referees' comments. Thewordfile contains the flast version of the paper. The Excel file contains all data and primers information These results, even if they need being refined, but already shed some light on the ecology of this host-parasite-vector system, together with the ecology of other pathogenic agents sharing the same cycle.