In this study, we identified and cloned the sea urchin Hemicentrotus pulcherrimus MT (Hp-MT) mRNA. We examined the gameto- and embryo-toxic effects and the expression of Hp-MT mRNA at various concentrations of phenol in H. pulcherrimus. We found that the normal embryogenesis rate was significantly inhibited when H. pulcherrimus was exposed to phenol (EC50 = 1565.86 ppb, 95% Cl = 1183.47-2037.84 ppb). The no observed effective concentration (NOEC) and the lowest observed effective concentration (LOEC) of the normal embryogenesis rate were < 10 ppb and 100 ppb, respectively. Hp-MT cDNA is 651 bp in length and encodes a protein of 64 amino acids. We found that the expression of Hp-MT mRNA was significantly increased with phenol treatment in a concentrationdependent manner. These results suggest that phenol at greater than 100 ppb has a toxic effect during the early embryonic stages of H. pulcherrimus, and MT mRNA may be used as a biomarker for risk assessment of phenol contamination.