Wild Pacific salmon, including Chinook salmon Oncorhynchus tshawytscha, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest, mitigation for hydroelectric development, and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. For policy implementation, a new approach to the assessment and management of Chinook salmon and the associated hatchery production and fisheries management are needed. Implementation of genetic stock identification (GSI) and parentage‐based tagging (PBT) for marine fisheries assessment may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of Chinook salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. GSI and PBT were used to identify Chinook salmon sampled in 2018 and 2019 marine fisheries (18,819 individuals genotyped) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 391 single nucleotide polymorphisms via direct sequencing of amplicons. Very high accuracy of assignment to population and age (>99.5%) via PBT was observed for 1994 Chinook salmon of ages 2–4 years, with a 105,722–individual, 380–population baseline available for assignment. Application of a GSI‐PBT system of identification to individuals in 2019 fisheries provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, with fishery exploitation rates directly comparable to those provided by CWTs for 13 populations. GSI and PBT provide an alternate, cheaper, and more effective method in the assessment and management of Canadian‐origin Chinook salmon relative to CWTs, and an opportunity for a genetics‐based system to replace the current CWT system for salmon assessment.

2013-2019_Chinook_brood_rubias

2018_Chinook_mixture_rubias

This is multi-locus genotype data for the Chinook collected in 2018. These were samples taken in fisheries. These are in Rubias format. The collection column describes the mixture for each sample, with lookup reference in Table S4. The individual column lists individuals in the format <analysis code>_<fishery year>_<julian catch date>_<fish number>.

2019_Chinook_mixture_rubias

This is multi-locus genotype data for the Chinook collected in 2019. These were samples taken in fisheries. These are in Rubias format. The collection column describes the mixture for each sample, with lookup reference in Table S5. The individual column lists individuals in the format <analysis code>_<fishery year>_<julian catch date>_<fish number>.