A study on ethnomedicinal use, preference for species, and ecological viability of plants used for treating malaria was carried out among the communities living around the Sango Bay Forest Reserve in southern Uganda. Semi-structured interviews and informal discussions were used to collect ethnobotanical information. Abundance and demographic patterns of the key forest tree species used to treat malaria were determined, using 45 plots of 0.1 ha. Sixteen species representing 11 families and 14 genera were reportedly used to treat malaria, including four new reports. Hallea rubrostipulata (K. Schum.) J.-F.Leroy, Warburgia ugandensis Sprague, and Syzygium guineense (Willd.) DC. were the most important forest tree species used to treat malaria and were chosen for further study. The three species were found to be highly valued in the treatment of malaria and similarly used by the local people as determined by the clustering procedure. The species generally had an inverse J-shaped curve in their population structures, indicating viable regenerating populations. The recognition of the use of traditional medicine by the local communities as an integral and essential part of their health care system is vital in the conservation and sustainable utilization of these plants.