Allyl isothiocyanate (AITC), is a natural compound found in plants belonging to the family Cruciferae and has strong antimicrobial activity and a biocidal activity against plants parasites. Anisakidosis is a zoonotic disease caused by the ingestion of larval nematodes in raw, almost raw, and marinated and/or salted seafood dishes. The aim of this work was to evaluate the effect of AITC against Anisakis larvae and to study its potential use during the marinating process. The effects of AITC against Anisakis larvae were tested in three experiment: in vitro with three liquid media, in semisolid media with a homogenate of anchovy muscle, and in a simulation of two kinds of anchovy fillets marinating processes. For all tests, the concentrations of AITC were 0, 0.01, 0.05, and 0.1%. Significant activity of AITC against Anisakis larvae was observed in liquid media, whereas in the semisolid media, AITC was effective only at higher concentrations. In anchovy fillets, prior treatment in phosphate buffer solution (1.5% NaCl, pH 6.8) with 0.1% AITC and then marination under standard conditions resulted in a high level of larval inactivation. AITC is a good candidate for further investigation as a biocidal agent against Anisakis larvae during the industrial marinating process.