Single Nucleotide Polymorphism (SNP) panels are powerful tools for assessing genetic population structure and dispersal of fish that can enhance management practices for commercial, recreational, and subsistence mixed-stock fisheries. Arctic Char(Salvelinus alpinus), Brook Trout (Salvelinus fontinalis), and Lake Whitefish(Coregonus clupeaformis) are amongst the top harvested and consumed fish species in northern Indigenous communities in Canada, contributing significantly to food security, culture, and economy. Genomic resources like SNP panels, however, have not been widely accessible to Indigenous fisheries managers. We developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses for three salmonids to support fisheries co-management in northern Canada. Using low-coverage Whole-Genome Sequencing data from 418 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec), and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were used to design GT-seq panels enabling high-throughput genotyping. Three GT-seq panels yielded an average of 413 autosomal loci and were validated with an average assignment accuracy of 98.5%. These GT-seq panels emerge as powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed stock fisheries across multiple regions. Interweaving these novel genomic-derived tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in northern Indigenous communities, contributing to food security programs and the economy in northern Canada.