The present invention is related with the isolation and cloning of a new gene, the production of the protein encoded by this gene by using recombinant systems, and the use of this antigen in a vaccine formulation as a purified protein and/or naked DNA, to induce an immune response in aquatic organisms against different ectoparasite species, including the known as sea lice, and pathogens associated with these infestations. The vaccine preparations, administered by oral route, immersion bath or injection, demonstrated its efficacy by producing IgM humoral immune response and reducing the number of parasites per fish in the vaccinated fishes.