SummaryThe survival and performance of 597 honey bee colonies, representing five subspecies and 16 different genotypes, were comparatively studied in 20 apiaries across Europe. Started in October 2009, 15.7% of the colonies survived without any therapeutic treatment against diseases until spring 2012. The survival duration was strongly affected by environmental factors (apiary effects) and, to a lesser degree, by the genotypes and origin of queens. Varroa was identified as a main cause of losses (38.4%), followed by queen problems (16.9%) and Nosema infection (7.3%). On average, colonies with queens from local origin survived 83 days longer compared to non-local origins (p < 0.001).This result demonstrates strong genotype by environment interactions. Consequently, the conservation of bee diversity and the support of local breeding activities must be prioritised in order to prevent colony losses, to optimize a sustainable productivity and to enable a continuous adaptation to environmental changes.