In order to establish genetic signatures for intraspecific identification, parts of the genes rbcL, rbcS and psbA and their intergenic spacer (IGS) regions were amplified by polymerase chain reaction (PCR) from the chloroplast genomes of Heterosigma akashiwo strains isolated from Japan. A transfer RNA-Leu gene trnL and a hypothetical gene cfxQ, which is related to ribulose bisphosphate carboxylase/oxygenase expression, were found in the upstream region of the rbcL gene and in the rbcS-psbA IGS region, respectively. All the gene-coding regions and the IGS regions between rbcL and rbcS showed the same sequences among the strains tested. In contrast, the rbcL upstream regions and the rbcS-cfxQ IGS regions showed some differences such as nucleotide substitutions, duplications and inversions between NIES-5 and the other strains. Based on these sequence data, five genetic signatures were established and their simple and rapid detection by means of strain-specific PCR primers and PCR-restriction fragment length polymorphism techniques was examined. The results suggested the usefulness of these genetic signatures and techniques for the discrimination of H. akashiwo populations.