In India, medicinal plants are often found in traditional agricultural systems such as home gardens, as scattered trees in croplands and on field risers. Characterization of species diversity in managed ecosystems and appraisal of the multiplicity of products and services in different agro-ecosystems were studied under the programme, "Multipurpose tree database for Agroforestry Research and Appropriate Management (MARAM)" on usage of biodiversity and ecosystems modified by human activity in south India. The MARAM database covered 269 tree species, which was recorded in the 544 farms sampled over 61 districts in six Agro-Ecological Zones (AEZs) of three south Indian states viz., Karnataka, Kerala and Tamil Nadu. All these species, which are reported by the landholders, are broadly classified based on nine major uses. However, 200 of these species are reported to have medicinal value in the literature, the landowners in our study area know only 85 species to be of medicinal use, and among them 8 are endemic to the Western Ghats, and 27 are exotic species. Around 58 indigenous species are regenerated naturally in the farmland, but landowners exploit these species for their valuable products, and for their medicinal uses. This paper discusses tree species diversity of the managed ecosystems, and traditional and ecological knowledge on tree uses.