BC’s interior tree fruit industry generates $130 million in wholesale revenue, contributes $900 million in economic activity, and directly employs 1,500 people annually. Ninety-five percent of the cherries grown in Canada are grown in BC and it is estimated that 80% of new cherry plantings in the world are varieties developed in BC by Agriculture and Agri-Food Canada. In order to maintain a global competitive edge new genomic research is underway to protect BC cultivars, as it is difficult to distinguish between similar varieties based on visual and taste characteristics alone. Summerland Varieties Corporation (SVC) is mandated with obtaining Plant Breeders’ Rights (PBR) and trademarks for varieties entering the marketplace to protect the assets of BC and Canadian growers. This project generated the first genome sequences for cherry and apple cultivars developed in BC, which will allow for the future development of genomic tools to help enforce PBRs for tree fruit cultivars developed from BC breeding programs. Genomic signatures for each variety will enable better protection in cases where there is a dispute between parties. The signatures are also expected to stimulate further research and development of new Canadian adapted varieties leading to a more nimble and sustainable industry.