The widespread availability of genomics data and molecular tools for pathogen detection and identification provides scientists and regulators a powerful toolbox for pathogen monitoring. However, this raises questions and concerns regarding the use of these tools in import and export of forest commodities. Discussions around implementation and standardization have highlighted knowledge gaps around their efficacy and suitability in wood and their applicability to forest commodities. This study compared detection efficacy of various emerging tools on artificially infected forest and wood commodities, focusing on Phytophthora pathogens, an important group of invasive and sometimes difficult to detect species. In situ detection was more sensitive than traditional isolation, and for some methods, 100% of infected samples were positive. Detection efficacy varied by tissue type and detection method. The data generated from this study is important in addressing knowledge gaps around pathogen detection in wood.