This dataset contains resequencing data used in our Arctic whale genomics research exaiming population structure and demographic history in bowhead whales and narwhal, including unfiltered genomic variants and filtered SNPs. Source code for genomic analyses is available at github.com/edegreef/arctic-whales-resequencing. Data uploaded here contain: bowhead_sample_info.csv - metadata for bowhead whale samples bowhead_RWmap_allvariants.vcf.gz - all variant calls in bowhead whales, including indels and SNPs (n = 21) bowhead_RWmap_snps.filtered.autosomes.vcf.gz - bowhead whale SNPs filtered for quality, bi-allelic sites, and autosomes (n = 21) bowhead_RWmap_snps.filtered.autosomes.hwe_maf_LDprunedr08_n20.vcf.gz - bowhead whale SNPs filtered for quality, bi-allelic sites, out of HWE, MAF > 0.05, LD-pruned, removal of close kin (n = 20). narwhal_sample_info.csv - metadata for narwhal samples narwhal_allvariants.vcf.gz - all variant calls in narwhals, including indels and SNPs for bowhead whales (n = 62*) narwhal_snps.filtered.autosomes.vcf.gz - narwhal SNPs filtered for quality, bi-allelic sites, and autosomes (n = 62*) narwhal_snps.filtered.autosomes.hwe_maf_LDprunedr08_n57.vcf.gz - narwhal SNPs filtered for quality, bi-allelic sites, out of HWE, MAF > 0.05, LD-pruned, removal of duplicates, close kin, and samples with high missingness (n = 57) The asterisk* is to note this includes 2 duplicate samples that were removed from the analyses and respective manuscript.