Domestication and artificial selection for desirable traits have driven significant phenotypic changes and left detectable genomic footprints in farmed animals. Since the 1960s, intensive breeding has led to the rapid domestication of Atlantic salmon (Salmo salar), with multiple independent events that make it a valuable model for studying early domestication stages and the parallel evolution of populations of different origins subjected to similar selection pressures. Some aquatic species, including Atlantic salmon, have undergone whole-genome duplication (WGD), raising the possibility that genetic redundancy resulting from WGD has contributed to adaptation in captive environments, as seen in plants. Here, we examined the genomic responses to domestication in Atlantic salmon, focusing on potential signatures of parallel selection, including those associated with WGD. Candidate genomic regions under selection were identified by comparing whole-genome sequences from aquaculture and wild populations across 2 independently domesticated lineages (Western Norway and North America) using a genome-wide scan that combined 3 statistical methods: allele frequencies (FST), site frequency (Tajima's D), and haplotype differentiation (XP-EHH). These analyses revealed shared selective sweeps on identical SNPs in major histocompatibility complex (MHC) genes across aquaculture populations. This suggests that a combination of long-term balancing selection and recent human-induced selection has shaped MHC gene evolution in domesticated salmon. Additionally, we observed selective sweeps on a small number of gene pairs in homeologous regions originating from WGD, offering insights into how historical genome duplication events may intersect with recent selection pressures in aquaculture species.