Technologies in forest molecular biology and tissue culture could play an increasing role in the choice of genotypes for successful establishment of agroforestry practices. Research areas such as micropropagation, somatic embryogenesis, genetic engineering, marker-aided selection, and molecular diagnostics are merging with traditional forest biological studies to help identify and produce better-suited trees for agroforestry plantings. A combination of classical and molecular biological research could be used to improve pest and stress resistance of selected genotypes, modify structure and function, and monitor pests of trees. This merger of approaches, as well as continued technological development, could accelerate the production and selection of suitable tree genotypes for agroforestry plantings.