We created a SNP genotyping array for Arctic charr (Salvelinus alpinus) featuring 86,504 single nucleotide polymorphisms derived from a diverse set of populations. Our goal was to develop a useful tool for a wide array of future studies, including the genetic improvement of aquaculture strains and the analysis of the evolutionary history of wild Arctic charr populations from diverse locations. To orient the SNPs and inform marker selection decisions, a draft reference genome was developed from sequencing of a single diploid female. The markers used in the design of the genotyping array were derived from a variety of sources. Eight charr made from crosses of Canadian Tree River and Nauyuk aquaculture strains were sequenced at ~40x genome coverage and reads were mapped back to the reference genome to identify SNPs. Reduced representation sequencing was performed on over 1000 fish including families derived from the Canadian Fraser, Nauyuk and Tree River aquaculture strains, the Icelandic lakes Þingvallavatn and Vatnshlíðarvatn as well as charr captured from lake Mývatn and nearby lava caves. These data were used for de novo identification of SNPs, which were then mapped on to the reference genome. Cross validation of SNPs from the different sources and comparison with published Arctic charr SNP records provided a set of markers that generalize across populations. Further candidate SNPs were identified based on criteria including minor allele frequency, association with functional genes, even spacing across intergenic regions, association with the sdY gene and utility in the study of specific populations.