Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (Sander vitreus) and sauger (Sander canadensis) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) SNPs clearly resolved walleye and sauger, and classified hybrids with high confidence. F₁, F₂, and multi-generation hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F₁ hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12/173 (7%) fish field-identified as pure walleye, and 1/24 (4%) identified as pure sauger were actually hybrids. In addition, 2/15 (13%) field-identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs, and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without pre-identification of informative loci, eliminating some of the key challenges associated with other marker types.