The honeybee Apis mellifera, major pollinator worldwide, is facing multiple threats to survival with the infestation by Varroa destructor being a major concern. Resistance to such infestation is a crucial mechanism for the maintenance of the honeybee population. However, to date, genetic components explaining this resistance are poorly known making selection for resistant honeybees a challenge. In this study we perform a genome wide association study on about 300 A.m. mellifera colonies for one trait measuring varroa resistance, the recapping of varroa infested brood cells. On about 300 A.m. mellifera colonies we identified multiple chromosome regions showing significant effects for this polygenic trait. We reported a heritability of 0.57 (±0.21). Recapping of varroa infested brood cells could be a trait of interest for the selection of resistant honeybees.