Genomic resources are under-developed for rodents, including well-studied species such as prairie dogs (Cynomys spp.). We conducted whole-genome resequencing on 10 Gunnison’s prairie dogs (C. gunnisoni, GUPD) and identified 12,842,055 high-quality SNPs, from which four sets of bait sequences were created. We designed two sets each (containing either 20k or 60k baits) for projects using contemporary (120 bp baits) or historical (100 bp baits) DNA. These bait sets can be used to study a variety of ecological and evolutionary questions in prairie dogs and other ground squirrel taxa.