Ethnobotanical studies and scorecard-based assessments have been used in identification and prioritisation of indigenous fruit trees with domestication and income potential at local levels. Less has been done to systematically identify species with potential for international markets. This study compared the applicability of the two methods to identify indigenous fruits with economic potential for export. The ethnobotanical study consisted of household and market surveys based on questionnaires, focus group discussions and key-informant interviews. The scorecard was based on pre-determined scoring criteria applied to species identified in the ethnobotanical study. Priority indigenous fruits identified in the ethnobotanical study included Canarium schweinfurtii, Vangueria apiculata, Garcinia buchananii and Tamarindus indica whereas the scorecard assessment identified a different set of species; i.e. V. apiculata, G. buchananii, Myrianthus arboreus, Pseudospondias microcarpa, Phoenix reclinata and Rhus vulgaris as having export potential. The ethnobotanical methods were effective in identifying species with local economic potential and hence high likelihood of adoption by local farmers while the scorecard method was found more useful to identify species with export potential.