The attainment of ever more sustainable agricultural production and reconciling agriculture with conservation are the main challenges that human beings are confronted with head-on in the future. Through expanding and enhancing agroforestry homegardens at the agricultural landscape level, biodiversity can be increased and maintained while addressing several utility values, ensuring both ecological and socioeconomic sustainability. This study was conducted in agroforestry homegardens of southern and southwestern Ethiopia, to examine plant species richness and other diversity indices, plant use, and classify and identify different types of homegardens based on their species composition and abundance. In total, 93 homegarden owners participated in the study. Two hundred and six (mean 15.44 per homegarden) different plant species (excluding weeds) that belonged to 161 genera and 66 plant families were identified across the studied sites. Fifteen species (about 7.28% of all species recorded) are endemic and threatened to Ethiopia. The overall mean plant species richness per agroforestry homegardens, mean individual density and other diversity parameters varied strongly among sites (P < 0.05). In all of the agroforestry homegardens, roots, and tubers food producing plant species tended to be more dominant (based on summed dominance ratio, SDR) than other species, except the cereal crops barley and maize. Based on cluster analysis, four groups of agroforestry homegardens were identified including, ‘small-sized, low plant diversity, barley-potato-enset-apple homegardens (Cluster-1)’; ‘intermediate-sized, taro-enset-coffee homegardens (Cluster-2)’; ‘large-sized, maize-taro-sweet potato-teff-enset homegardens (Cluster-3)’; and ‘small-sized, high plant diversity with mixed-use category homegardens (Cluster-4)’. The results also indicate that agroforestry homegardens as ecological niches are valuable for the conservation and maintenance of biological diversity both for crop genetic as well as forest tree resources, including harboring of endemic and threatened species in those human-dominated landscapes.