Hard clams is one of the important farmed shellfish in Taiwan. It was belongs to the phylum Mollusca, class Bivalvia, order Veneroida and family Veneridae. Only depending on the shell morphology is difficult to identify correctly. However, much of the clam classification to date is based on shell characteristics. In order to identify correctly, we have to work with DNA sequence data. On the other hand, population structure of hard clams is still not very clear in Taiwan. Therefore, the information about the amount of genetic variation within and among population is important for further clams broodstock management and utilization. In this year, we analyze 62 microsatellite primer sets from the published reference of Meretrix hard clam. Only two 2 primer sets can identify the hard clam from Tamsui or Yunlin. Analysis the ITS gene by next generation sequencing, the results show that the major sequences of ITS gene is OTU1 and the percentage is 76%-97% of hard cam in Taiwan. According to the structure analysis, the genetic structure is quite simple and show the lower individual differences of the hard clam from Japan. The genetic structure is more complex and show the higher individual differences of hard clam in Taiwan.