Background Equine trypanosomiases are complex infectious diseases with overlapping clinical signs defined by their mode of transmission. Despite their economic impacts, these diseases have been neglected by the scientific community, the veterinary authorities and regulatory organizations. To fill the observed knowledge gap, we undertook the identification of different trypanosome species and subspecies naturally infecting horses and donkeys within the Chadian sleeping sickness focus. The end objective, being to investigate the potential role of these domestic animals as reservoirs of the human infective Trypanosoma brucei gambiense Method Blood samples were collected from 155 donkeys and 131 horses in three human African trypanosomiasis (HAT) foci of Chad. Rapid diagnostic test (RDT) and capillary tube centrifugation (CTC) test were used to search for trypanosome infections. DNA was extracted from each blood sample and different trypanosome species and subspecies were identified with molecular tools. Results From 286 blood samples collected, 54 (18.9%) and 36 (12.6%) were respectively positive for RDT and CTC. PCR revealed 194 (67.8%) animals with trypanosome infections. The kappa Cohen coefficients used to evaluate the concordance between the diagnostic methods were low; ranging from 0.087±0.04730 to 0.48 ± 0.06951. Trypanosomes of the subgenus Trypanozoon were the most prevalent (29.4%), followed by T. congolense forest (11.5%), T. congolense savannah (4.9%) and T. vivax (4.5%). Two donkeys and one horse from the Maro HAT focus were found with T. b. gambiense infections. Between animal species and HAT foci, no significant differences were observed in the infection rates of different trypanosomes. Conclusion This study revealed several trypanosome species and sub species in donkeys and horses, highlighting the existence of AAT in HAT foci of Chad. The identification of T. b. gambiense in donkeys and horses suggests considering these animals as potential reservoir for HAT in Chad. The presence of both human-infective and human non infective trypanosomes species highlights the need for developing joined control strategies for HAT and AAT.