Most studies undertaken in the field of agroforestry have focussed on system design, soil fertility management, and system interactions. Less emphasis has been placed on biodiversity aspects. The aim of this study is to investigate the potential of indigenous, multistrata agroforests for maintaining native woody species diversity in the south-eastern Rift Valley escarpment, Ethiopia. A total of 60 farms, representing three agroforest types (enset-AF, enset-coffee-AF and fruit-coffee-AF), were randomly selected along altitudinal gradients. Enset (Ensete ventricosum) is a perennial, herbaceous monocarpic banana-like plant which serves as a food plant in Ethiopia. The three agroforests are results of the domestication of natural forests and intensification of the landuse systems centuries ago. Sample-based assessment protocols were employed to place sample quadrats and to measure all individuals in the quadrats. A total of 58 woody species, belonging to 49 genera and 30 families, was recorded. Of all woody species identified, 86% were native. The highest proportion of native woody species was recorded in enset-AF (92%), followed by enset-coffee-AF (89%) and fruit-coffee-AF (82%). Among native tree species, Millettia ferruginea and Cordia africana were the most widespread. In all, 22 native woody species were recorded as of interest for conservation, acccording to IUCN Red lists and local criteria. Among them, Pygeum africanum and Rhus glutinosa were categorised as vulnerable in the wild, and in need of conservation priority. The introduction of non-native fruit trees in agroforests can be a threat to maintenance of native woody species. Management strategies favoring enset and coffee will also put other native tree species at risk. A smaller number of native woody species was recorded in fruitcoffee-AF, but a higher mean basal area and stem number. The mean basal area and stem number ranged from 5.4 ± 0.5 to 11.7 ± 1.0 m 2 ha -1 and 625 ± 84 to 1,505 ± 142 stems ha -1 , respectively. Altitude explained 68 and 71% of the variation in species richness and abundance, respectively. Finally, it is concluded that recognition of the indigenous agroforestry system as an option for maintaining native woody species should be given more attention, to counteract the local threat of these species from the wild.