Although a diversity of trypanosome species have been detected in various animal taxa from human African trypanosomosis (HAT) foci, cattle trypanosomosis has not been addressed in HAT foci of west and central African countries including Chad. This study aimed to determine the prevalence of pathogenic trypanosome species in cattle from three HAT foci of the south of Chad. Blood samples were collected from 1466 randomly selected cattle from HAT foci of Mandoul, Maro, and Moïssala in the south of Chad. For each animal, the sex, age and body condition were recorded. Rapid diagnostic test (RDT) was used to search Trypanosoma brucei gambiense antibodies while the capillary tube centrifugation (CTC) test and PCR-based methods enabled to detect and identify trypanosome species. From the 1466 cattle, 45 (3.1%) were positive to RDT. The prevalence of trypanosome infections revealed by CTC and PCR-based method were respectively 2.7% and 11.1%. Trypanosomes of the subgenus Trypanozoon were dominant (6.5%) followed by T. congolense savannah (2.9%), T. congolense forest (2.5%) and T. vivax (0.8%). No animal was found with DNA of human infective trypanosome (T. b. gambiense). The overall prevalence of trypanosome infections was significantly higher in animal from the Maro HAT focus (13.8%) than those from Mandoul (11.1%) and Moïssala HAT foci (8.0%). This prevalence was also significantly higher in animal having poor body condition (77.5%) than those with medium (11.2%) and good (0.5%) body condition. The overall prevalence of single and mixed infections were respectively 9.4% and 1.6%. This study revealed natural infections of several pathogenic trypanosome species in cattle from different HAT foci of Chad. It showed similar transmission patterns of these trypanosome species and highlighted the need of developing control strategies for animal African trypanosomosis (AAT) with the overarching goal of improving animal health and the economy of smallholder farmers.