Bees play a major role in agriculture yet have been under decline. Major colony losses are largely attributed to bee-specific infectious diseases and even though some diseases can be controlled using chemical pesticides, many of the bacteria, viruses, fungi, and mites responsible are finding ways to resist these. Integrated Pest Management (IPM) is the combination of a variety of approaches to control and manage agricultural pests and/or diseases; it can include biological, physical, cultural, mechanical, behavioural, and chemical controls. This project aimed to develop new IPM tools and recommendations: 1) honeybee stock with natural disease resistance selected using molecular fingerprints, 2) treatments for bee diseases that should be absolutely specific for the pathogens, and 3) best-practices guidelines for IPM based on existing tools and the two new ones to be developed here. The successful implementation of the results of this project would result in at least $200 million in annual benefits to Canadian agriculture based on the expected decrease in colony losses, increased honey production and greater availability of bees for pollination. Consumers, crop growers and beekeepers will benefit from improved food security and healthier, more abundant, more effective pollinators.