The indigenous communities from Vaupes Medio possess knowledge in the use of plants to treat their illnesses. This knowledge has been transmitted orally from generation to generation. The present article aimed to carry out investigates the ethnobotany of medicinal plants used to cure malaria by 10 knowledgeable indigenous communities from Vaupes Medio, Colombia. Open and semi-structured interviews were conducted with 33 traditional healers representing 10 indigenous communities located in the Colombian southeast. Concurrently, field trips were conducted to identify and collect the reported species. Together with the aid of a bibliography, the identification and gathering of information for each species was performed in the Colombian Amazonian Herbarium -COAH -Sinchi Institute, Colombian National Herbarium (COL) and University of Antioquia Herbarium (HUA) herbariums. To find the relative importance of each plant species used to treat malaria, the degree of consensus among the survey respondents was determined using the Friedman's index. The traditional healers reported 41 morphospecies, among them 35 were identified down to the species, 5 to the genus, and 1 to the family. Notably, only we have reported 28 of these morphospecies for antimalarial use. Also, the plants that presented a major relative importance were Abuta grandifolia, Aspidosperma excelsum, Matisia cf. glandifera and Pleonotoma jasminifolia. Despite social and cultural changes favoring the rapid decline of ancestral knowledge, these indigenous communities located in the southeast of Colombia, have still managed to conserve their knowledge and use of traditional medicine to cure malaria.