Honey bees are a crucial part of Canadian agriculture, contributing at least $4.6 billion/y: they produce between eighty and ninety thousand tonnes of honey each year and their pollination activities directly support the production of many fruits, nuts and vegetable crops. But the health of honey bees has been declining over the past decade, with Canadian beekeepers losing more than a quarter of their colonies each winter since 2006-07. We often replace these colonies by purchasing bees and queens from offshore but we cannot rely on these sources because of the risk of importing new diseases or invasive strains of honey bees (such as the Africanized ‘killer’ bee). The high colony losses, coupled with the possible loss of access to replacement sources, pose a serious threat to the productivity of major Canadian agri-food industries and jeopardize our food security. Left unchecked, the production and accessibility of fruits, nuts and vegetables will decline. Our team of researchers will improve the health of Canadian honey bees by developing new genomic and proteomic tools that will enable beekeepers to rapidly and cost-effectively breed healthy, disease-resistant, productive bee colonies that are better able to survive our harsh Canadian winters. The availability of high-quality, locally bred honey bees should reduce Canada’s dependence on imported queens. In parallel, we will increase the safety of bee importations by developing an accurate and cost effective assay to detect bees with Africanized genetics. Our research team will work with a large number of beekeepers across five provinces, industry technology-transfer teams, diagnostic labs and government regulators to ensure that our ‘omic tools are implemented and accessible to the beekeeping industry by the end of the project. Our innovative efforts aim to help guard the safety and sustainability of the beekeeping industry, ensuring our food security and supporting billions in value to the Canadian economy.