Chinook salmon are widely distributed across the globe with native stocks in the North Pacific Ocean and self-sustained populations introduced to regions in the Northern and Southern Hemispheres. Pacific salmon are economically and ecologically important to the Pacific Northwest, USA, yet several wild populations are federally listed as endangered or threatened due to depleted stocks, loss of genetic diversity, and hatchery contribution to wild stocks. As such, fishery managers are concerned with successful identification of mixed origin Chinook salmon stocks, as well as the health and condition of hatchery-origin fish and their impacts on wild populations. Therefore, this thesis examines ways to improve stock discrimination to provide a more useful tool for fishery managers. In Chapter 2, I found that otolith shape variation of Chinook salmon is a useful tool for stock classification in three case studies at different spatial scales. First, Chinook salmon otoliths from native and introduced ranges were contrasted across the Northern and Southern Hemispheres. Second, I compared otolith shape at basin-level within wild populations in western Oregon and naturalized populations in southern South America. Third, I compared otolith shape between hatchery and wild-origin Chinook salmon within the Elk River, Oregon. I adapted a simple machine learning model for stock discrimination that used otolith shape variation as well as additional morphometric information to successfully separate Chinook salmon groups within each case study. In addition to stock discrimination, fish otoliths are often used to test for differences in symmetry as otoliths aid in hearing, homing, and balance. In Chapter 3, I found higher asymmetry of morphological characters between left and right sagittae in hatchery-origin Chinook salmon stocks than in wild stocks. Results from these studies have conservation and management implications as hatchery-origin Chinook salmon can reduce pressure from wild stocks while continuing to support commercial and recreational industries. Otolith shape analysis is a promising tool for stock discrimination if used in conjunction with other methods to better understand life history plasticity of anadromous species like Chinook salmon.