It is known in vertebrates that endothelin-1 (ET-1) plays a key role in morphogenesis whose expression level greatly influences the development of craniofacial malformations. In the present study, the complete cDNA fragment encoding a precursor of endothelin-1, the preproendothelin-1 (PPET1), was cloned by RACE-PCR from European sea bass. The cDNA encoded a 199 amino acid polypeptide that was composed of the “mature” and “big” ET-1. Relative ET-1 expression levels were investigated in European sea bass larvae fed microparticulate diets containing the standard amount (0.08 g retinol/kg diet: group N) or an excess of retinoic acid which induces skeletal malformations (0.5 g retinol/kg diet: group RA). Real-time reverse transcription polymerase chain reaction analysis revealed that PPET1 mRNA levels were sensitively reduced in the RA group during early development (days 10 and 15 post hatching). Regulation of ET-1 gene expression in larvae fed the teratogenic level of vitamin A confirmed the involvement of ET-1 in the molecular mechanism involved in craniofacial deformities. These results suggest that the expression level of ET-1 may be used as a precocious molecular marker to predict malformations during European sea bass development.