Technical Abstract: Glycyrrhiza lepidota Pursh (Fabaceae; American wild licorice), is a nitrogen-fixing, perennial, facultative riparian species present along many dryland rivers in western North America, including the U.S., southern Canada and northern Mexico. Like Glycyrrhiza glabra, common licorice native to Europe, Central Asia and China, Glyccyrhiza lepidota has been used to treat coughing, hoarseness, and sore throat. Knowledge of the extent, distribution, and structure of the North American Glycyrrhiza species genetic diversity can provide a tool for breeders to exploit and improve its medicinal qualities. The objective of this study was to assess the genetic diversity and structure within and among populations along two different river environments in the Northwest. We sampled 10 populations along a 30 mile stretch of the Snake River in a mostly wide open and relatively linear environment. We also sampled 5 populations along 50 miles of the Salmon River in a narrow, canyon-like environment accessible mostly by raft. Amplified fragment length polymorphism (AFLP) and Targeted Region Amplified Polymorphism (TRAP) markers were used to measure genetic diversity. The TRAP markers were designed to target regions in the genome corresponding to metabolites specific to Glycyrrhiza. STRUCTURE analysis of the Snake River populations showed a large, panmictic population, while Salmon River populations were more distinct from one another, as well as from the Snake River populations. River environments can have an effect on genetic diversity, likely from isolation of populations from pollinators. Interestingly, the largest populations along the Snake River were the most similar within and differentiated somewhat from the smaller populations; possibly as a result of restricted dispersal of pollinators from an abundant source.