The multiplex PCR system including six microsatellites from Haliotis discus hannai, consisting of dinucleotide and trinucleotide repeat units, is developed. The six loci were coamplified in a single reaction employing dye-labeled primers. Alleles from these loci were sized using an internal standard by automated sample processing in an ABI3100 Genetic Analyser. Amplified alleles in profiles containing selected microsatellites were typed clearly, providing easily interpretable results. In this results suggest that the presented multiplex PCR system may be a useful tool in a selective breeding program of H. discus hannai in which genetic identification will allow different genotypes to be reared together from fertilization. This should have a great impact as it will make selective breeding more efficient. Moreover, it will be useful in a variety of applications, including strain and hybrid identification, parentage assignment, pedigree reconstruction, estimating genetic diversity and/or inbreeding.