Selective breeding programs in aquaculture species have provided huge gains in a variety of commercially important traits. Many breeding designs require an explicit understanding of the pedigree of the brood stock animals, this can be kept using physical tags or using molecular reconstruction. Here we develop a low density SNP panel for parentage assignment in Atlantic Salmon (Salmo salar) using RAD-seq data. The steps for filtering and designing a SNP panel form a workflow that allows for researchers to develop their own panels of SNPs for parentage in any species.