Honey bees, Apis mellifera, have experienced the full impacts of globalisation, including the recent invasion by the parasite Varroa destructor, hereafter called varroa. This deadly mite has rapidly become one of the main causes of colony losses worldwide, with a huge economic impact on beekeeping. Despite the lethal effects of varroa, some colonies survive infestation. In such colonies, honey bees are able to develop defence strategies that limit mite spread and confer colony resistance to varroa. In some populations, resistance traits were found to be sufficiently heritable to offer sustainable opportunities to fight varroa infestations through selective breeding of naturally resistant honey bees. Recent advances in genomics allow for the development of new tools to assess the importance of genetic mechanisms involved in varroa resistance. Here we report on the largest genome-wide association study performed on honey bees to understand the genetic basis of multiple phenotypes linked to varroa resistance in Apis mellifera. Genome wide association studies for varroa resistance traits were performed on whole genome sequencing of more than 1,500 colonies belonging to three different genetic backgrounds and combined in a meta-analysis. Results show that varroa resistance is largely polygenic in nature, involving many genes with small effects. Still, a total of 60 genetic markers were identified as having a significant impact on varroa resistance in at least one of the honey bee populations tested. These associations pinpoint several regions of the honey bee genome that are linked with varroa resistance phenotypes and increase our understanding of the mechanisms underlying honey bee resistance to its main parasite. Our results will also support the building of strategies for genomic selection in honey bee breeding.Competing Interest StatementThe authors have declared no competing interest.