Grapevine virus disease management has been identified by the grape grower and wine industries as a top priority for long‐term sector sustainability. Losses of over $23 million per year are currently incurred by grape growers due to reduced yield of infected grapes and increased fruit rejection by wineries. To replace the currently infected acreage and meet ongoing renewal of vineyards the industry needs access to 6.7 million domestically produced, virus free vines/year. There will be two separate pathways for implementation and commercialization. To accommodate these demands, the Canadian Food Inspection Agency (CFIA) Sidney Centre for Plant Health (CPH) requires a rapid, cost effective genomic solution to replace the over 30 molecular and bioassays currently performed on , which can take up to three years to complete. By implementing a high throughput sequencing method at the CFIA the costs of analysis will be reduced and analysis time will be reduced for industry priority varieties imported into Canada as well as audit testing from certified foreign sources destined to commercial planting. Reducing the testing time to 10 days allows grape growers to rapidly improve the health of their vineyards. Domestically, the Canadian Grape Certification Network (CGCN) is commercializing high throughput sequencing through its partner Cool Climate and Oenology Viticulture Institute for the certification of propagation material in nurseries and grapevines obtained through CPH, and for monitoring of production vineyards.