Salmon production in Canada is under increasing threats from infectious and non-infectious diseases such as complex gill disease. Over the last decade gill health and associated disease has been a growing challenge in salmon farming operations in both the Pacific and North Atlantic. Complex gill disease is a multifactorial condition resulting from the interaction of environmental and husbandry conditions as well as infection by pathogens and parasites to create proliferative lesions, particularly during the summer and fall months. This project will validate biomarkers of healthy and compromised gills of Atlantic salmon and use these to develop an early warning system for the development of gill disease on Atlantic salmon production sites across Canada. The resulting genomics-enabled tools for fish health will guide the management and intervention strategies for complex gill disease in Atlantic salmon.