The major contamination sources, biofilm-forming ability and biocide resistance of Staphylococcus aureus in tilapia-processing plants were evaluated. Twenty-five processing control points were analysed twice in two factories, including whole tilapias, frozen fillets, water and food-contact surfaces. No final product was contaminated with S. aureus. However, high concentrations of S. aureus carrying enterotoxin ( se) genes were found in several processing points of both factories due to the application of inadequate hygienic and handling procedures, which generate a high risk of cross-contamination of the tilapia fillets with staphylococcal enterotoxins. Nine S. aureus strains were characterized by RAPD-PCR using primers AP-7, ERIC-2 and S. A wide diversity of se gene profiles was detected, most strains being multi- se-carriers. All S. aureus strains showed high biofilm-forming ability on stainless steel and polystyrene. Biofilm-forming ability was correlated with the presence of fliC H7 and the type of origin surface (metallic or plastic). A marked resistance of S. aureus to peracetic acid and sodium hypochlorite was also observed, required doses being higher than those recommended by manufacturers to be eradicated. Case-by-case approaches are thus recommended to determine the sources and degree of contamination present in each factory, which would allow applying precise responses that avoid, or at least reduce, the presence of bacterial pathogens and the emergence of antimicrobial resistance.