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Human-related environments, including food and clinical settings, present microorganisms with atypical and challenging conditions that necessitate adaptation. Several cases of novel horizontally acquired genetic material associated with adaptive traits have been recently described, contained within giant transposons namedStarships.While severalStarshipshave been recently found in domesticated species, the extent of their impact on the evolution of human-associated fungi remains unknown. Here, we investigated whetherStarshipshave shaped the genomes of two major genera of fungi occurring in food and clinical environments,AspergillusandPenicillium.Using seven independent domestication events, we found in all cases that the domesticated strains or species exhibited significantly greaterStarshipcontent compared with close relatives from non-human-related environments. We found a similar pattern in clinical contexts. Our findings have clear implications for agriculture, human health and the food industry as we implicateStarshipsas a widely recurrent mechanism of gene transfer aiding the rapid adaptation of fungi to novel environments.