Stock-specific migration-timing and relative abundance of exploited fish species are critical parameters to estimate for management of mixed stock fisheries. Here, we used parentage-based tagging (PBT) together with mixed stock analyses (MSA) to estimate stock-specific abundance and migration-timing in anadromous adult steelhead (Oncorhynchus mykiss) sampled at Bonneville Dam in the lower Columbia River. Results indicate that natural-origin steelhead was represented by 11 of 13 possible stocks found throughout the Columbia-Snake river basins, while hatchery-origin steelhead was primarily composed of five stocks from the Snake River drainage. Further, migration-timing differentiated stocks and allowed categorization of early, intermediate, and late migrating stocks. Analyses of age and length data for these stocks also showed that late-arriving fish were larger due to older age and originated primarily from the Clearwater River, South Fork Salmon River, and Dworshak Hatchery, all from the Snake River drainage. Sex ratios tended to be skewed towards females and ranged from 51.5 to 68.9% for hatchery stocks and 60.5–71.8% for natural-origin stocks. This suggests that anadromous migration is favored by females while males are more likely to residualize in freshwater. Overall, this study demonstrates how the use of PBT in MSA can reveal important stock-specific differences in migration-timing and relative abundance and provides critical information for management of mixed stock fisheries.