A key consequence to the process of taking organisms into captivity for human use, often with artificial selection of beneficial traits, is domestication. Attention to the domestication of fish has been increasing from the beginning of the 20th century in association with the rapid growth in aquaculture. One such species that typifies the wider growth in aquaculture, as well as domestication, is the Atlantic salmon (Salmo salar). Here we assess the impact of domestication on Atlantic salmon morphology and microbiome using a common garden design, whereby fish from different genetic backgrounds including wild, domesticated and reciprocal wild x domesticated hybrids (as well as F2 hybrids and backcrosses) are reared together from the eyed-egg stage. Key phenotypes have been examined, both internal and external, relating to morphology and microbiome. Our pedigree controlled experimental design and use of an array of hybrids has demonstrated genetically additive domestication driven changes, with 1) reduced fork length adjusted kype height in domesticated fish, 2) increased fork length in domesticated fish, 3) increase pectoral fin length in domesticated fish, 4) reduced eye width in domesticated fish and 5) altered body shape in domesticated fish, when compared to wild counterparts - with hybrids showing intermediate phenotypes). In addition to this, the application of both artificial and natural common gardens has highlighted that domestication driven morphological changes are quickly removed from populations through strong stabilising selection to a wild optimum, likely due to reduced fitness. The results shown here not only demonstrate the rapid (~ 12+ generations) total phenotypic changes caused by artificial selection, it also highlights the risks posed to wild populations from aquaculture escapees and introgression. Such findings reinforce the need for continued innovation in preventing fish escapes from aquaculture.