Hard clams are important farmed shellfish in Taiwan. They belong to the phylum Mollusca, class Bivalvia, order Veneroida and family Veneridae. Only depending on the shell morphology is difficult to discriminate 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. 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 will construct the sequence library of internal transcribed spacer from culturd hard clams by next generation sequencing and analysis the genetics diversity and try to undrstand the intra-species genetics information of wild hard clams from different area in Taiwan. In this year, we collected the wild clams from Tamsui, Changhua, Chiayi and Kinmen. The co2 gene sequence of those clams were belong to the Meretrix spp. After analyzed the co2 gene, the wild and farmed hard clams are the same species. The optimal annealing temperature of PCR is 62℃, the primer was designed based on the ITS sequence of M. meretrix、M. lusoria、M. petechialis from NCBI database. According to the NGS and genetic diversity analysis, the ITS sequence diversity of hard clams in Tamsui show no significant difference.