Traditional medicinal plants have played a major role in the enhancement of health care in developing countries around the world. Ethiopia has been practicing traditional botanical medicine for the curing of human biological, mental or physical disorders. Ethno botanical study was carried out to survey medicinal plants and their uses for malaria control in Assosa district. Information was collected from 150 medicinal plants users and traditional medicine healers via interviewer-administered questionnaires. The informants were selected randomly from four different villages of Assosa district, Southwestern Ethiopia. A total of 11 species of ethno botanical medicinal plants used for malaria control were identified. Of eleven ethno botanical plants, Allium sativum and Echinops kebericho were majorly used for malaria treatment and vector prevention in Assosa district. Leafs were the mostly used part of the plant and most of the medicinal plants were used for treating infections. The indigenous knowledge and practice of traditional medicinal plants in the study area were at risk of getting lost. The communities in the current study area practiced traditional ethno botanical medicine for malaria therapy and disease prevention. The indigenous practices contributed to the sustained use, management and protection of medicinal plants and multiple-use of ethno botany/indigenous trees. The current study suggests that similar studies in areas not previously covered should be carried out in order to get a full picture of the country’s medicinal plants potential in the future.