A study on edible and medicinal indigenous plants was conducted to highlight the current state of traditional knowledge on the medicinal and food uses of indigenous plants in Burundi. The data were obtained through a review of the literature and documents related to the ethnobotanical studies of the flora of Burundi. Ethnobotanical indices allowed us to highlight the information contained in these data. 20 flagship species were identified on the basis of their high use value, their nutritional and phytochemical value validated by scientific references. Innovations on indigenous edible and medicinal plants of Burundi, especially in the field of pharmacy, could be implemented to enhance the biological resources of Burundi as well as the traditional knowledge of the Burundian population. Following the gradual decrease of native plants in anthropogenic environments, programs for the domestication of these plants accompanied by sustainable management measures must be strengthened in order to reinvigorate the transmission of knowledge of the uses of native plants and to ensure the sustainability of raw materials for the pharmaceutical industries. A similar study could be undertaken to show the state of knowledge of edible and medicinal native plants for domestic animals.