Pantoea stewartii subsp. stewartii is a pathogenic bacterium that causes Stewart’s wilt in corn. Stewart’s wilt is a disease that is indigenous to North America and has been occasionally reported in other parts of the world. It is a disease of major phytosanitary importance and many different countries worldwide have imposed importation restriction on seed imports to prevent potential introduction of the pathogen. Phytosanitary restrictions that are imposed are often only described to restrict movement of Pantoea stewartii as a species. However, Pantoea stewartii consists of two different subspecies, Pantoea stewartii subsp. stewartii and Pantoea stewartii subsp. indologenes. Pantoea stewartii subsp. indologenes is a bacterium that is occasionally found on corn seed as a part of the resident bacterial population; it is not a pathogen of corn and is not a regulated pathogen worldwide. Current accepted laboratory testing methods used to detect Pantoea stewartii, enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR), were not designed to quickly distinguish the two Pantoea subspecies. Novel real-time PCR assays have been developed to specifically target intergenic DNA sequences that allow Pantoea stewartii subsp. stewartii to be detected from corn seeds and also be distinguished from the nonpathogenic Pantoea stewartii subsp. indologenes. National plant protection organizations worldwide should adopt these new real-time PCR testing techniques to provide a quick, efficient and accurate detection of Pantoea stewartii subsp. stewartii. Adopting testing on a subspecies level would increase testing efficiencies, reduce costs, and reduce incidence of false positive testing results. This in turn could also could also potentially increase export volumes to existing countries that receive US corn exports.