Declines in bee populations across the world threaten food security and ecosystem function. It is currently not possible to routinely predict which specific stressors lead to declines in different populations or contexts, hindering efforts to improve bee health. Genomics has the potential to dramatically improve our ability to identify, monitor and predict the effects of stressors, as well as to mitigate their impacts through the use of marker-assisted selection, RNA interference and potentially gene editing. Here we discuss the most compelling recent applications of genomics to investigate the mechanisms underpinning bee population declines and to improve the health of both wild and managed bee populations.