Food insecurity in the Canadian North is a serious problem. This is particularly true for remote communities where store bought food is prohibitively expensive; approximately 70% of households in Nunavut report to be food insecure, which is nearly 10 times the national average in Canada. In these regions, subsistence harvesting has been a desirable, viable, and culturally important contribution to food security in the past, but is becoming increasingly challenging due to the rising cost of equipment, fuel, and maintenance, conflicting work hours, and less predictable conditions on the land. Consequently, additional economic opportunities are often sought after to afford rising food costs and provide valuable jobs to the community. One such opportunity is the development of small scale commercial and subsistence fisheries. Here we discuss the community driven research method used by the Towards a Sustainable Fishery for Nunavummiut project in the community of Gjoa Haven, Nunavut. Traditional and local knowledge from active hunters are part of an integrated knowledge co-production process paired alongside a broad scale characterization of fish genomics and microbial diversity. Community members are involved in the design and re-design of research objectives and biological sampling as preliminary results are obtained.