A two stage sampling ethno-pharmacological study was carried out with agro-pastoralists in Nakasongola district involving two sub-counties namely; Nabiswera and Nakitoma. Participatory methods were used to establish a livestock disease inventory, ethno-diagnosis, medicinal plants used and implication for livestock-based livelihoods. Fourteen focus groups discussion comprising of 198 persons and 32 key informant interviews were conducted. Trypanosomosis (20.9%), East cost fever (15.5%) and helminthosis (12.8%) were found to be the most prevalent of the twenty five diseases affecting different livestock species in the area. Thirty seven plants species belonging to 28 genera and 24 families were reported as traditional treatments against helminthosis. The frequently used plant parts were leaves (54.1%) and roots (29.7%). Cold aqueous extraction (pounding and adding water) (81.1%) was the main method of preparation of ethno-veterinary remedies with oral drenching as the main route of administration. About 65% of population used combination of traditional and conventional veterinary medicine, 22% used only conventional veterinary medicines, while 13% of the farmers used traditional medicine. Accuracy of ethno-diagnosis compared well with conventional veterinary medicine diagnosis although the causes of the diseases were not well understood by the respondents. Medicinal plants were found to be an important input in livestock production although their efficacy, active molecules and safety is not known thus there was urgent need of scientific studies into these research gaps.