This dataset contains resequencing data used in our killer whale genomics research exaiming population structure and demographic history, including unfiltered genomic variants and filtered SNPs. Source code for genomic analyses is available at github.com/edegreef/killerwhale-resequencing. Data uploaded here contain: orca_sample_info.csv - metadata for the killer whale samples orca_unfiltered_diploid.vcf.gz - all variant calls, including indels and SNPs (n = 29) orca_snps_q30_biallelic.vcf.gz - SNPs filtered for quality and bi-allelic sites (n = 29) orca_snps_q30_biallelic_HWE0.005_miss0.4.vcf.gz - SNPs filtered for quality, bi-allelic sites, out of HWE, and missingness > 0.4 (n = 29). orca_snps_q30_biallelic_HWE0.005_miss0.4_maf0.05_LDprunedr08_n24.vcf.gz - SNPs further filtered for MAF, LD-pruned, and removal of kin & duplicates (n = 24).