Over the past 10 years, the aquaculture industry in the province of Newfoundland and Labrador (N.L.) has experienced significant growth (to 1500 per cent). However, one of the major health challenges for this industry is sea-lice, which limits industry growth and compromises sustainability. Lice infestations are one of the biggest problems in salmon aquaculture today costing the producer up to $150 CAD per tonne produced each year in losses and treatments. In 2017, the Newfoundland Aquaculture Industry Association (NAIA) through industry consultations identified integrated pest management strategies for sea lice control as the number one ranked industry priority for N.L.’s salmon aquaculture sector. A successful strategy to control sea lice is the utilization of cleaner fish, i.e., lumpfish (Cyclopterus lumpus) and cunner (Tautogolabrus adsperus). The use of cleaner fish was deemed a high priority by all of N.L.’s salmon companies — Cooke Aquaculture Inc., Northern Harvest Seafarms Limited, Grieg N.L. and Marine Harvest Atlantic Canada. The use of cleaner fish is attractive because they reduce the use of chemotherapeutants, and are less stressful to the fish. The number of cleaner fish used by the worldwide salmon farming industry has increased exponentially since 2008, and it is estimated that 50 million cleaner fish will be required by 2020. Commercial production of cleaner fish is an emerging industry that has the potential to generate many new jobs. Memorial University’s Ocean Sciences Centre (OSC) is North America’s leading cleaner fish R&D facility. However, industrial production faces challenges due to the lack of knowledge about the biology of these fish species, limiting the rapid growth of this emerging industry. Susceptibility of lumpfish and cunner to bacterial infectious diseases, lack of a vaccination program, and lack of broodstock production programs, are the major challenges facing cleaner fish production for use in aquaculture biocontrol. C. lumpus and T. adspersus are on the list of the 100 fish gold standard genomes to be sequenced, and the sequence of these fish will contribute to fundamental biodiversity knowledge, and fill a critical gap in fundamental knowledge that will allow the development of specific vaccination programs and accelerate commercial production of an emergent aquaculture sector. In this proposed research, we will sequence the whole genome of C. lumpus and T. adspersus and profile the global gene expression response to vaccination and bacterial infection. The specific objectives are to: i) sequence the genomes of C. lumpus and T. adspersus; ii) develop a cohabitation bacterial infection model and profile the gene expression of infected C. lumpus and T. adspersus; and iii) profile the gene expression of vaccinated C. lumpus and T. adspersus and assess commercial and improved (in-house) vaccine efficacy. We expect to generate the critical knowledge that will help accelerate the growth of the commercial cleaner fish industry in Canada and contribute to the development of vaccination and breeding programs.