The National Clonal Germplasm Repository (NCGR) in Davis is one among the nine repositories in the National Plant Germplasm System, USDA-ARS, that is responsible for conservation of clonally propagated woody perennial subtropical and temperate fruit and nut crop germplasm. Currently the repository holds over 6500 accessions of germplasm of Actinidia (kiwi fruit), Diospyros (persimmon), Ficus (fig), Juglans (walnuts), Morus (mulberry), Olea (olive), Pistacia (pistachio), Prunus (stonefruits and almond), Punica (pomegranate), Vitis (grape), and other minor genera. Wild relatives are widely represented in these collections with about 91% of the taxa and 43% of the total accessions representing the wild gene pools. Research at the repository is mainly focused on genetic characterization of germplasm using molecular markers and morphological traits to quantify and describe genetic structure and differentiation within and among species and gene pools. Promoting the use of crop wild relatives (CWR) germplasm in genetic improvement of tree fruit and nut crops is our top priority. Presently, at the Davis repository, we are extensively utilizing Prunus and Juglans wild relatives for developing improved rootstocks with resistance to biotic and abiotic stresses. We will review and discuss the results of ongoing programs highlighting the importance of different CWRs as donors of genes for resistance to major soil borne diseases such as crown gall, Phytophthora rots, and nematodes in the rootstock improvement programs. Breeding for drought tolerance is another major thrust for which we are screening CWR germplasm to identify novel sources of drought tolerance to infuse into ongoing rootstock breeding programs.