<p dir="ltr">This item contains four datasets.</p><p dir="ltr">Microsatellite_genotypes: Raw microsatellite genotypes.</p><p dir="ltr">Raw_haplotype_sequences: Aligned mitochondrial DNA control region haplotype sequences generated in this study.</p><p dir="ltr">Sample_sizes: Sample size of the three markers used, the demographic groups and sex of the whales, and the time period and decades in which the samples were obtained.</p><p dir="ltr">Research_data_summary: Details of the samples used in this study, including sample code, year of collection, sex, mitochondrial DNA (mtDNA) control region haplotype, carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) ratios sampling location. The “St HB to MB” location is between St. Helena Bay and Mossel Bay. An asterisk (*) denotes the samples with a heterozygous base pair.</p>