Bacterial canker, caused by <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i>, is an economically devastating seed-borne pathogen that inflicts considerable damage throughout all major tomato-producing nations. Understanding the movement of <i>C. michiganensis</i> subsp.<i> michiganensis</i> both microscopically and geographically will help characterize population diversity, virulence, and modes of infection. In order to investigate the mode of seed infection, New York <i>C. michiganensis</i> subsp. <i>michiganensis</i> field strains were stably transformed with eGFP. <i>C. michiganensis</i> subsp. <i>michiganensis</i> was able to access the developing seeds either i) systemically through the xylem and/or ii) externally by entering fruit through lesions on the pericarp. <i>C. michiganensis</i> subsp. <i>michiganensis</i> cells were located within the developing seed, endosperm, and funiculus, although at relatively low levels compared with the large numbers of cells observed in xylem and pericarp cells; thereby, highlighting the difficulty in detecting and eradicating small initial pathogen populations within seed lots. Furthermore, multilocus sequencing typing revealed a high level of <i>C. michiganensis</i> subsp. <i>michiganensis</i> diversity in New York with approximately 20 unique sequence types. Unique differences were also evident in virulence and plasmid profiles.
