High throughput sequencing (HTS) provides a rapid, comprehensive and efficient approach for viral pathogen identification. Recent studies found HTS superior to conventional methods for detecting viruses of economic significance in grapevine and fruit trees. In addition to conventional detection methods, HTS is now an important component of routine testing procedures at Foundation Plant Services (FPS) at the UC-Davis for plant material citification and quarantine import programs. In 2017, FPS obtained a new import permit which provides for the potential provisional quarantine release with USDA-APHIS approval of plant material with no viral agent(s) detected by HTS analysis. When HTS is used in conjunction with current conventional methods, growers of certified and registered material can initiate propagative increase and virus elimination programs with new accessions years earlier. While HTS remains a powerful new technology with significant benefits for plant certification and quarantine programs, there are challenges to consider. Since detecting a given pathogen sequence does not mean that pathogen is responsible for the disease, establishing biological significance for viruses identified via HTS analysis is necessary. In addition, efficient sample preparation methods for large scale application and bioinformatics algorithms to efficiently separate pathogen and host sequences must be developed, validated, and standardized across laboratories. No regulatory decision can be made on the importance of a novel virus without information on its biological effects.