In 2002, Clavibacter michiganensis subsp. michiganensis (Smith) Davis, the causal organism of bacterial canker of tomato (Lycopersicon esculentum), was isolated from two of six commercial asymptomatic tomato seed lots produced on Java in Indonesia. C. michiganensis subsp. michiganensis has not been reported in Indonesia previously. Methods based on the protocol of the International Seed Health Initiative were used to extract and identify the presence of C. michiganensis subsp. michiganensis in tomato seed. C. michiganensis subsp. michiganensis was isolated with dilution plating on the semiselective media D2ANX and mSCM. The identity of the colonies was confirmed by immunofluorescence microscopy, polymerase chain reaction (2), fatty methyl ester analysis, enzyme-linked immunosorbent assay based on monoclonal antibody 103 (1), and a pathogenicity test in which three replicate tomato plants were stem inoculated with 108 cells ml-1. Within 2 weeks, stripes on stems developed that split and exposed reddish brown cavities (stem cankers). The presence of C. michiganensis subsp. michiganensis poses a direct threat on tomato production, which is one of five economically most important vegetable crops in Indonesia.