The richness of Canada’s biodiversity is under threat today due to climate change, habitat destruction and novel emerging diseases. A common thread across conservation strategies is the need for genomic tools to address knowledge gaps related to species evolution, adaption, viability, and genetic diversity. A reference-quality whole genome sequence is the foundation for such genetic analysis and the subsequent development of these management tools. The Canadian BioGenome Project will lead Canada’s contribution to these efforts and will raise Canada’s profile in the field of conservation genomics. The goals of the project are to identify species that are of specific relevance to Canada where genomic information and tools will be important to generate and develop policy recommendations for application of genomics to conservation and monitoring.