BACKGROUND : The application of ethnobotanical indigenous knowledge is very important in improving primary healthcare systems among the local communities living around and within protected areas in South Western Uganda. In this area, there are biodiversity endowed Queen Elizabeth National Park (QENP), Maramagambo Central Forest Reserve (MCFR) and Ihimbo Central Forest Reserve (ICFR). Despite the rich floral diversity and cultural heritage, there is no published documentation on the use of medicinal plants in this area. This information can be used as a basis for the selection of medicinal plants for further phytochemical and pharmacological studies. OBJECTIVE : This study identified and documented the use of medicinal plants, plant parts used, and mode of preparation and administration by the local communities living around and within QENP, MCFR and ICFR. METHODS : A cross-sectional study was used to collect data from 202 informants using semi-structured questionnaires, open interviews and field visits. Ethnobotanical data was analyzed using use reports (UR), frequency of citation (FC) and Informant Consensus Factor (FIC). The plants species were identified by botanists and voucher specimens were deposited. RESULTS : A total of 302 medicinal plant species were mentioned by informants, out of which only 211 species belonging to 65 families and 165 genera were collected, identified and documented. The remaining 91 species were not available for collection and informants stated that they had become very rare within the study area. Herbs (35.8%) were the main source of herbal medicine. Leaves (60.4%) were the most commonly used plant parts used in the preparation of herbal remedies. Most of the medicinal plants were harvested from the wild, either growing in abundance (41%) or as rare species (21%). The most common mode of administration was oral, while other exceptional modes such as touching with bare hands and sweeping over the affected part were reported for the first time. The medicinal plant species were reported to treat 134 physical ailments, which were grouped into 16 ICPC-2 disease categories. Digestive disorders (854 UR) and general and unspecified disorders (507) scored the highest FIC value of 0.83. The highest number of medicinal plants (146 plant species) was used for treatment of digestive disorders. Among the species with higher use reports, Gouania longispicata had the highest frequency of citation (FC = 174) and was mentioned to be used to treat 41 physical ailments. The most important ailment treated by Gouania longispicata was allergy with 102 use reports. CONCLUSIONS : A variety of medicinal plants are used by communities living near protected areas in South Western Uganda. Most species were used in the treatment of digestive disorders, followed by general and unspecified disorders. Much as allergy has not been identified as a major threat by the health sector in Uganda, the study found out that it is one of the prevalent ailments in the study area. While the therapeutic value of some of the documented medicinal plant species, especially those with higher frequency of citation have been scientifically validated, the efficacy and safety of other species with wide application need to be investigated. In this study, we recommend further scientific studies on Gouania longispicata to validate its wide usage in the study area.