Mitochondrial DNA of three laboratory strains of Penaeus monodon from Malaysia, Australia and Fiji and one farm population of P. japonicus were analysed. The molecule size of the mtDNA of the two penaeid species was similar and close to 16 000 base pairs. The polymerase chain reaction method provided molecular markers of species identity which showed a high interspecific diversity. According to RFLP data in P. monodon, a genetic divergence of 1.68% was found between the Fiji strain and the Australia/Malaysia strains. This result yielded new genetic data about the Indo-West Pacific biogeographical region. A restriction map of the mtDNA of the Fiji strain was established and the small ribosomal subunit gene region was located. The farm population of P. japonicus was structured but, because its parental origin was unkown, it was not possible to determine intraspecific variation.