Pathogen detection and identification have been vastly improved with advances in genomics; however, knowledge gaps remain around efficacy and use in wood commodities, especially in regulatory settings. In part one of this project, we compared detection efficacy of different methods on common export and import forest products. In-situ detection was more sensitive than traditional isolation, with 100% detection rates for some methods. However, there were several false positives in control samples. False positive detection of quarantine pathogens on wood products could be a serious problem in trade. The goal of part two of this project was to determine the cause of the false positives. In addition, we continued to compare detection methods by looking at point of care detection with a portable qPCR system and using RNA assays to test pathogen viability. False positives were likely due to DNA contamination persisting through the various wood processing steps. These results confirm the need for additional confirmation of pathogen presence or viability after a positive DNA test. RNA assays failed to detect pathogen presence in most samples. Further testing is needed to determine optimal RNA extraction conditions to provide meaningful results. Point of care detection using portable tools was comparable to laboratory methods and would provide a useful tool for pre-screening commodities for the presence of quarantine pathogens.