Molecular epidemiological analysis of Kudoa septempunctata isolates from 34 olive flounders associated with foodborne disease outbreaks and from 6 reference samples was performed using random amplified polymorphic DNA (RAPD) analysis. The K. septempunctata isolates analyzed in this study were divided into 8 groups. Eight isolates obtained from the large Ehime Prefecture outbreak in Japan that had occurred on October 8, 2010, were further divided into 4 groups. Eight isolates obtained from Korean samples were divided into 3 groups. These groups included isolates that had been identified from the large Ehime Prefecture outbreak. These results indicated that the Korean isolates had similar genetic backgrounds to those involved in the Ehime Prefecture outbreak. Isolates associated with outbreaks with similar dates of onset tended to be classified in the same group, suggesting that the strains involved in these incidents were genetically related. These results demonstrated that RAPD analysis is a useful molecular epidemiological analysis method for K. septempunctata.