A large quantity of the jellyfish, Aurelia aurita, invade cooling water systems and cause serious problems at several electric power stations in Japan. In the present study, we examined intra—species genetic variation of A. aurita in Wakasa Bay, Japan in order to estimate the original polyp habitat of the adult medusae invading electric power stations. Total DNA was extracted from the adult medusae and the wild polyps, and polymerase chain reaction (PCR) was performed using the specific primers for amplification of nuclear internal transcribed spacer one (ITS-1) and mitochondrial cytochrome oxidase c subunit 1 (CO1). Then the DNA sequences of the PCR products were compared. The results showed genetic polymorphism of A. aurita in Wakasa Bay and locally specific frequency of each haplotype. The haplotype frequency, especially in CO1, of the adults collected at one of the power stations in Wakasa Bay was similar to that of the polyp colonies at harbours in the embayed area, not at another harbour in the western entrance of the bay. The polymorphic analysis is, therefore, thought to be useful for the determination of original polyp habitat as source of the adult medusae in relatively limited regions such as Wakasa Bay.