Honeybees, Apis mellifera, have experienced the full impacts of globalisation, including the recent invasion by the parasitic mite Varroa destructor, now one of the main causes of colony losses worldwide. The strong selection pressure it exerts has led some colonies to develop defence strategies conferring some degree of resistance to the parasite. Assuming these traits are partly heritable, selective breeding of naturally resistant bees could be a sustainable strategy for fighting infestations. To characterise the genetic determinism of varroa resistance, we conducted the largest genome wide association study performed to date on whole genome sequencing of more than 1500 colonies on multiple phenotypes linked to varroa resistance of honeybees. To take into account some genetic diversity of honeybees, colonies belonging to different ancestries representing the main honeybee subspecies in Western Europe were included and analysed both as separate populations and combined in a meta-analysis. The results show that varroa resistance is substantially heritable and polygenic: while 60 significant associations were identified, none ex-plain a substantial part of the trait genetic variance. Overall our study highlights that genomic selection for varroa resistance is promising but that it will not be based on managing a few strong effect mutations and rather use approaches that leverage the genome wide diversity of honeybee populations. From a broader perspective, these results point the way towards understanding the genetic adaptation of eusocial insects to parasite load.