Hard clams is one of the important farmed shellfish in Taiwan. It belongs to the phylum Mollusca, class Bivalvia, order Veneroida, family Veneridae. Only depending on the shell morphology is difficult to identify them correctly. However, much of the clam classification to date is based on shell characteristics. In order to identify them correctly, we have to work with DNA sequence data. At present, the mitochondrial gene can provide the maternal genetic information, but the paternal information is still unclear. This project is to establish the paternal genetic information of ITS gene by next generation sequencing. The results show the hard calms is not purebred and hybrid in certain extent in Taiwan. We can get the DNA sequece information by the non-lethal sampling technique. Furthermore, the DNA can be extracted from the 1987's shell periostracum. The analysis of mtDNA sequence show the hard clams form Taiwan and Japan were clustered into two groups. This means that the hard clams from Taiwan and Japan's M. lusoria should be two species.