American ginseng (Panax quinquefolius) is a valuable medicinal herb threatened by over-harvest. Because data are insufficient, current attempts to protect diversity and improve cultivation are inadequate. Random Amplified Polymorphic DNA (RAPD) markers were used to estimate genetic diversity and high-performance liquid chromatography (HPLC) was used to characterize root ginsenoside concentrations in wild and cultivated populations of American ginseng in Maryland. Wild populations were less diverse than cultivated and highly differentiated from one another; suggesting that drift was high and gene flow low in wild populations. Exotic plants were genetically and phytochemically distinct from native plants. The main ginsenoside in exotic plants was Re versus Rg1 in native plants. Plants from at least one wild population were genetically and phytochemically similar to exotic plants, suggesting that exotic plants were introduced into wild populations. Thus, native Maryland American ginseng is unique but threatened by drift, isolation and artificial introductions.