Fish products are considered a nutritionally significant component of the human diet. Accordingly, 200 different commercial fish product samples (25 each of canned solid tuna, canned chunks tuna, canned crumbled tuna, canned anchovy, canned mackerel, canned sardine, herring, and tilapia fillets) of different brands were collected from various local and high supermarkets in Aswan City during 2020-2021. The samples were subjected to microbial quality assessment, and PCR was carried out to detect some virulence genes of fish-borne pathogens to evaluate the control measures for food safety. The results presented that the highest bacterial loads (cfu/g) in the examined fish products were proven in fillets tilapia (1.3×104±0.32) and herring (1.0×104±1.2) while anchovy, mackerel, and crumbled tuna were the highest anaerobic count with means of 7.3×103±1.2, 7×103±1.6 and 6.7×103±1.4, respectively. The prevalence of P. aeruginosa occurs with an incidence of 29%. The lasB gene (50%) has been the most detected virulence gene, followed by exoS (40%). V. parahaemolyticus was present in 7.5%, and the regulator toxin genes (toxR and L.tdh) were found in 33.3% and 22.2%. Additionally, 20% of the samples had A. hydrophila, and the aerA and act genes were found in 60% of the isolates. In addition, C. perfringens was detected in 33% of examined products, and the virulence genes cpa and etx were present and discovered to be a proportion of 20% and 50%, respectively. The current study concluded that the examined fish products possess one or more food poisoning virulence genes.