Methylfarnesoate (MF), an analogue of the insect juvenile hormone III, has been implicated to play a vital role in the regulation of the growth and reproductive development in crustaceans. Farnesoic acid O-methyltransferase (FAMeT) is the key enzyme involved in catalyzing the final step in the MF biosynthetic pathway. In this study, we report the cloning and characterization of the cDNA encoding the putative FAMeT of the shrimp Metapenaeus ensis. FAMeT comprises 280 amino acid residues with a predicted molecular weight of 32kDa. The predicted putative FAMeT protein reveals a high degree of structural conservation of FAMeT with the lobsters. It shares 79 and 70% sequence identities with the putative FAMeTs of Homarus americanus and Panulirus interruptus, respectively. As revealed by the Southern blot analysis and genomic PCR, only one gene exists in the shrimp genome and the gene is uninterrupted in the coding region. The shrimp FAMeT mRNA is widely distributed in many tissues with the highest expression level observed in the central nervous system. A constant level of FAMeT expression is recorded in the ventral nerve cord of the juveniles and the mature females during the reproductive cycle. Unlike the ventral nerve cord, the eyestalk of the juvenile male, but not the female, expresses FAMeT. Further study shows that the eyestalk of the mature female expresses FAMeT during all stages of ovarian maturation. We speculate that FAMeT may be important for the regulation of eyestalk neuropeptides. This is the first extensive study on the molecular characterization, structural analysis and expression of the crustacean FAMeT.