OBJECTIVE: To evaluate Trypanosoma brucei gambiense infection in peri-domestic livestock from Kogo and Mbini foci (Equatorial Guinea) in order to investigate its possible implication in the sleeping sickness transmission cycle in these hypoendemic foci. METHODS: Samples from 698 domestic animals (goats, sheep and pigs) from trypanosomiasis-endemic localities of Kogo and Mbini foci were tested for animal trypanosomes and T. b. gambiense (group I) by species-specific polymerase chain reaction. RESULTS: Trypanosoma brucei s.l., the predominant trypanosome species, was detected in 182 (52.6%) samples from Mbini and in 127 (36.1%) samples from Kogo. T. b. gambiense was only identified in seven (2%) of the Mbini samples and one co-infection (with T. vivax) was observed. CONCLUSION: The occurrence of T. b. gambiense in peri-domestic livestock in Mbini and its absence in Kogo could explain the epidemiological differences between the two foci and could have significant implications for sleeping sickness control in Equatorial Guinea.