BACKGROUNDSurveillance of "silent" human African Trypanosomiasis (HAT) foci is important for the achievement of the World Health Organization (WHO) goal of interrupting the transmission of this disease by 2030. It is in this context that this study was carried out to determine the trypanosome species circulating in the "silent" HAT foci of Bafia and the Manoka island in Cameroon.METHODSIn the Bafia and Manoka HAT foci, georeferenced pyramidal traps were used to trap tsetse flies. After DNA extraction from each whole fly, molecular tools were used to detect different trypanosome species as well as the origin of tsetse fly blood meals. Geographical information system was used to map the trypanosome infections and entomological data and to localize areas at high risk for trypanosome transmission.RESULTSFor this study, 1683 tsetse flies were caught and the relative apparent densities was 2.96: 0.03 in the Bafia HAT focus and 5.23 in the Manoka island. For the molecular identification of trypanosomes, 708 non-teneral tsetse flies (8 from Bafia and 700 from Manoka) were randomly selected. The overall trypanosome infection rate was 7.34 % with no infection in the Bafia HAT focus. Among the analysed flies, 4.57 % had trypanosomes of the subgenus Trypanozoon while 4.1 % and 1.13 % had respectively T. congolense and T. vivax. The most common mixed infections were the combination of trypanosomes of the subgenus Trypanozoon and T. congolense. Of the 708 tsetse flies analysed, 134 (18.93 %) tsetse flies were found with residual blood meals, 94 % and 6 % were respectively from humans and dogs. The trapping sites of Plateau, Sandje and Hospital appeared as the areas where contact with tsetse flies is most common.CONCLUSIONThis study revealed a discrepancy in the abundance tsetse flies as well as the trypanosome infection rates in tsetse of the two "silent" HAT foci of Cameroon. The detection of different trypanosome species in tsetse from the Manoka Island highlights their transmission. The high percentage of human blood meals in tsetse flies indicates an important contact between tsetse flies and human; emphasizing the risk of trypanosome transmission to human in this island.