Tree improvement has revolutionized agroforestry in terms of producing hybrid clones with a wide range of functional traits such as cold and drought tolerance, disease resistance, and higher biomass production (timber and fodder) within a limited period. Understanding the yield potential of woody components has helped farmers select tree species of improved planting material for their agricultural fields. Species like poplar and eucalyptus have proved a boon to farmers as these species have strengthened the economic status of farmers through agroforestry. Assessment of promising clones and their performance in particular regions have made agroforestry successful. The expansion of clonal plantations has reduced pressure on natural forests. The crown architecture of clonal trees has recorded higher foliage efficiency than that of seedling-raised trees, which is an important determinant of under-story light availability for agricultural crops. Clonal plants also have higher physiological efficiencies, providing better photosystem protection from cellular oxidative stress in the hot, dry climate due to higher antioxidant activities. Hybrid clonal evaluation has been investigated in waterlogged soils, riparian buffers, and degraded soils of managed agricultural landscapes. Clonal agroforestry is the promising and most sustainable way to produce food and wood in the current scenario of climatic adversities. The upcoming market for farmers is on the way to fetch income in terms of carbon credits for offsetting carbon emissions. The current challenge is to produce site-specific clones that ultimately determine the quality and quantity of production. Hence, in this chapter, we summarize the paradigms of clonal forestry in the different areas of interest in agroforestry.