A repetitive sequence-based (rep)-polymerase chain reaction (PCR) and inter-simple sequence repeat (ISSR)-PCR were used to molecular type Pseudomonas syringae pv. syringae (PSS) strains isolated from barley and wheat plants with bacterial black node symptoms grown in 22 different locations and six different seed-production districts in Japan. Eighteen genomic fingerprinting (GF) genotypes were obtained from the combined results of BOX-, REP-, and GTG(5)-PCR, indicating that the PSS population in Japan has high genetic diversity. The result based on logistic regression indicated that the population of GF genotype A was significantly related to a seed-producing district and that the epidemic of PSS strains in fields originated mainly from seed infection. This study will be applicable to future studies of the molecular epidemiology of bacterial plant diseases that have multiple infection routes.