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ABSTRACT Objective Maintaining population diversity is essential for the sustainable management of fish populations. In mixed-stock fisheries, this requires managers to target harvest on abundant stocks while minimizing impacts on co-migrating stocks of concern—a challenge that depends on detecting spatiotemporal differences in migration patterns. The objective of this study was to identify and characterize differences in marine timing and migration route through marine approach areas for Fraser River Sockeye Salmon Oncorhynchus nerka at a resolution commensurate with ecologically and genetically distinct groupings, or conservation units (CUs). Time series of CU-specific migration data will both inform stock assessment models used for this fishery and help guide decision making for more selective harvest strategies. Methods Reconstructed daily marine abundances provided by the Pacific Salmon Commission were used to derive novel time series of marine timing, migration route around Vancouver Island, and migration overlap for 11 different Fraser River Sockeye Salmon CUs. Models were developed to test for, and quantify, CU-specific differences in marine migration characteristics and to identify other key biological covariates that could be used to reliably describe these CU-level data. Results Statistically significant differences in Fraser River Sockeye Salmon migration behavior were observed as a function of CU, reconstruction location, and relative CU composition. Many CUs exhibited cyclic patterns in migration behavior, with earlier marine timing and lower rates of northern migration around Vancouver Island observed every 4 years (e.g., 2004, 2008, 2012, …, 2020). Despite significant spatial and temporal separation in the migration of some Fraser River Sockeye Salmon CUs, other CUs showed less behavioral differentiation and a high degree of overlap. Conclusions In the face of ongoing population declines, management tools that help preserve stock diversity are critical to supporting the long-term resilience of Fraser River Sockeye Salmon. A deeper understanding of CU-level diversity, including behavioral traits like marine timing and migration route selection, provides a foundation for adaptive management strategies that can sustain both fisheries and vulnerable populations under changing environmental conditions. Improvements to predictions of marine timing and migration route using CU-specific time series, and accounting for cyclic changes in behavior, can help inform preseason fisheries planning and can be used to explore impacts of potential fisheries openings and closures. However, even with perfect knowledge of fish behavior, mixed-stock management tactics such as spatial and temporal closures in marine areas will only be effective for a subset of Fraser River Sockeye Salmon CUs that exhibit predictably distinct differences in patterns of migration behavior. Managers will have to look to other approaches to help balance conservation objectives with harvest opportunities where CUs with various levels of conservation concern display strong overlap in migration distributions.