The blue mud shrimp (Upogebia pugettensis) is a vital ecosystem engineer in estuaries along the west coast of North America. Under normal circumstances, this species fulfils several important roles, including nutrient cycling, estuary aeration, and habitat provision for a number of commensal species. Unfortunately, nearly all populations of this species have undergone an extreme decline in recent years due to the anthropogenic introduction of an invasive isopod parasite (Orthione griffenis). In order to preserve U. pugettensis for the sake of estuary health, the population structure of the species must be considered. However, the genetic distribution of U. pugettensis is almost entirely unknown. This study analyses the population structure of the blue mud shrimp through genomic sequencing, PCA, TESS, and isolation-by-distance analyses, based on the supposition that at least one major genetic barrier exists for this species along its natural range. Results indicated the presence of one major and one minor genetic barrier for this species within the range of locations sampled: the larger barrier is present in northern California, while the less defined barrier is located near northern Washington. Isolation-by-distance did not play as important a role in determining U. pugettensis’ population structure; however, a moderate amount of genetic variation in the species could still be attributed to physical distance. From this, conservation implications and future research on U. pugettensis are discussed, providing insight into the preservation and recovery of this endangered species.