Biodiversity of the world is reducing over time since human interference in the natural forest is increasing progressively. However, there is alternative land use system that can save diversity of organisms at the same time when providing products for subsistence and commercial. Accordingly, Agroforestry provides eco-agricultural solutions that successfully combine objectives for increased food security and biodiversity conservation gains, especially by promoting greater use of native tree species in agroforestry systems like coffee shade system which have been promoted as one of the agricultural practices that host diverse plant. Particularly in Africa, few studies of biodiversity in human made landscapes such as coffee agroecosystems have been conducted. From the study conducted on the traditional coffee production system and adjacent natural forests, endangered tree species like Cordia africana is the dominant species in the shade coffee system. From this point, there is hope for biodiversity conserving from extinction through expanding shade coffee production system, particularly, tree species.