Brook charr Salvelinus fontinalis is a salmonid species of importance for conservation, aquaculture and sports fisheries. Salvelinus is also an under-represented branch of family Salmonidae in terms of genomic resource availability. Using genotyping-by-sequencing (ddRAD PstI and MspI) on a mapping family of 192 full-sib offspring, we generated a high-density linkage map containing 3863 markers for brook charr.