Successful honey bee breeding programmes require traits that can be genetically improved by selection. Heritabilities for production, behaviour, and health traits, as well as their phenotypic correlations, were estimated in two distinct Swiss Apis mellifera mellifera and Apis mellifera carnica populations based on 9 years of performance records and more than two decades of pedigree information. Breeding values were estimated by a best linear unbiased prediction (BLUP) approach, taking either queen or worker effects into account. In A. m. mellifera, the highest heritabilities were obtained for defensive behaviour, calmness during inspection, and hygienic behaviour, while in A. m. carnica, honey yield and hygienic behaviour were the most heritable traits. In contrast, estimates for infestation rates by Varroa destructor suggest that the phenotypic variation cannot be attributed to an additive genetic origin in either population. The highest phenotypic correlations were determined between defensive behaviour and calmness during inspection. The implications of these findings for testing methods and the management of the breeding programme are discussed.