Within the last two decades substantial progress has been made in understanding seed bank dynamics and the contribution of the soil seed bank to a post-disturbance plant community. There has been relatively little progress, however, in understanding perennial bud bank dynamics and the contribution of the soil bud bank to secondary succession. This lack of information is due primarily to the inability to reliably identify roots, rhizomes, and lignotubers that lie dormant beneath the soil surface. This scientific investigation, therefore, addressed the issue of identification of belowground woody structures. The first objective was to develop a methodology that utilizes molecular tools to reliably identify woody plant species from subsoil tissue samples. The second objective was to create a key in which molecular markers serve as criteria for identification and differentiation of selected tree and shrub species common to the mountains of northeast Oregon and southeast Washington. Application of restricted fragment length polymorphism (RFLP) analysis on polymerase chain reaction (PCR)-amplified rbcL gene products proved to be a reliable method to identify and differentiate 15 plants to the genus level. Two restriction enzymes, DPN II and Hha I, cut (or do not cut) the PCR-rbcL product into one to six fragments. Fragment number and length are used to develop an identification key. Plants not analyzed in this key may share the same banding patterns , resulting in a false-positive identification of unknowns. Future research needs and management implications are discussed.