These data comprise restriction site-associated DNA sequencing (RADseq) data generated using RAD capture for 260 wild-caught brook trout (Salvelinus fontinalis) from 8 waterways along the Minnesota shoreline with Lake Superior and 94 domestic brook trout representing 9 hatchery strains. RADseq libraries were prepared following the methods of Ali et al. (2016 Genetics) and used in a single RAD capture reaction then underwent PE150 sequencing on an Illumina HiSeq X.