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. The purpose of this project is to investigate the diversity of the hard clams in Taiwan, constructing the database of bio-barcode, clarifying the phylogenetic relationship and to assist the breeding study and conservation management. The bio-barcode fragment is 631bp, the PCR primer was designed form the coI gene sequence. The hard clem samples were corrected from the New Taipei City, Changhua, Yunlin, Chiayi, Tainan, Kaohsiung and Kinmen. Total 161 biobarcode sequence were corrected in the bio-barcode database. In this study, we first report that the M. lusoria could be identified quickly by coII gene sequence. Through the sequence aligment and phylogenetic analysis of the mitochondrial coI and coII gene sequences, M. lusoria is the main current hard clam species in Taiwan.