AbstractA workflow for developing a cost‐ and time‐efficient, single nucleotide polymorphism (SNP)‐based assay for species and hybrid identification is described. In a reference set (n = 46), the developed assay identified individuals of two closely related species, the Atlantic salmon (Salmo salar L., n = 23) and brown trout (Salmo trutta, n = 23), with 100% accuracy. Furthermore, species and hybrid identification using field‐collected embryos had 98.1% concordance (155/158) to more expensive and time‐consuming methods that utilized multiple SNP markers. The method can be integrated into management and conservation plans to quantify species' spawning distribution and hybridization rates.