ZP protein is a family of proteins which possess a conserved ZP domain and generally play an important role in the fertilization process. In this study, a new ZP cDNA from Branchiostoma japonicum, which codes 927 amino acid residues, was found. By using SMART software, it was confirmed that the ZP protein contains three domains (ZP Domain, Transmembrane Domain and Low Complexity Region). Furthermore, the sequence diversity of this ZP gene inBranchiostoma japonicumpopulation was analyzed. As a result, the ZP sequences amplified from 9 Branchiostoma japonicum individuals are 2 481-2 784 bp, which code 826-927 amino acids. There are 55 variable cites (5.93%, 55/927) identified by amino acid sequence alignment. 9 and 101 amino acids fragment deletion in two individuals may be due to the diverse alternative splicing of ZP gene. In conclusion, the sequence diversity of ZP proteins may be correlated with its structure and function diversity.