Kenya is home to some 600,000 donkeys that are found virtually in all ecological zones where they provide transport and draught power. In the Lamu archipelago where there is no motorised transport, donkeys are virtually the only available means of transport helping to transport farm produce, building materials and for getting from one place to the next. This study was conducted in April (dry season) and November 2009 (wet season) in four villages in Pate Island to investigate the prevalence and species of trypanosomes infecting donkeys and to identify the fly vectors playing a role in the transmission of trypanosomosis. Blood samples were collected from 288 and 319 donkeys and examined by buffy coat technique (BCT) and Giemsa stained blood smears. Trypanosomes were encountered in 3.1 and 7.5% of the examined donkeys in the dry and wet season respectively and there was no difference in the prevalence between villages during both seasons (p=0.159 and 0.709) but there was a significant difference (p=0.006) between seasons. Three species of trypanosomes detected were, in order of predominance were Trypanosoma congolense Broden (68.7%), Trypanosoma vivax Ziemann (21.8%) and Trypanosoma brucei Plimmer and Bradford (6.2%). Another 6.2% were mixed infections. There difference in mean PCVs between trypanosome infected and non-infected donkeys dry and wet seasons ranging significant to highly significant (p<0.05 and p<0.001) respectively. Trypanosome infection had a significant effect on mean body condition score of the donkeys during both seasons (p<0.05 and p<0.001). Prevalence of trypanosome infection was found to be independent of sex and age. However, mean PCV was significantly associated with age, sex and body condition scores. The entomological surveys revealed the presence of Glossina pallidipes Austen and other biting flies namely Stomoxys spp Linnaeus, Tabanus spp. Linnaeus, and Haematopota spp Linnaeus. Though the use of BCT for detection of trypanosomes in the field is almost universal, it has limited application especially in chronic infections and the field samples are in the process of being analysed using PCR to give a more accurate picture of the prevalence and as it relates to health and productivity of donkeys.