Canada’s forests and urban trees cover over 400M ha, providing an array of economic and environmental benefits. Invasive alien species are an increasing threat that can cause irreversible damage to the environment and are responsible for losses of hundreds of millions of dollars to the Canadian economy, impacting agriculture, forestry, urban and natural environments, as well as international trade. This has become an urgent issue spurred on by unprecedented levels of international trade and a changing climate. Two species that represent urgent threats to Canada’s forest and agricultural resources are the Asian gypsy moth and Phytophthora ramorum, a fungus-like pathogen. One of the major challenges in preventing their introduction and spread is the ability to rapidly detect and identify them in their various life stages. We develop DNA detection arrays that target different genomic regions for rapid and accurate identification and their sources. The final milestone consists in the deployment of these tools within the Canadian Food Inspection Agency operations.