As global attention intensifies on sustainable food systems, the safety of fish as a major protein source demands critical scrutiny. This study offers a detailed microbiological evaluation of commonly consumed fish species available in the Egyptian market, emphasizing both the extent of contamination and the potential of natural preservation strategies. Bacteriological analysis revealed notable disparities in microbial load across species and tissues. Bagrus bajad showed the highest surface contamination by Enterococcus species, while Oreochromis niloticus exhibited the lowest counts consistently in both surface and muscle tissues. In muscle samples, Mugil cephalus carried the highest levels of Enterococcus and psychrotrophic bacteria. Pseudomonas species was most abundant in Bagrus bajad, and least in Oreochromis niloticus. Salmonella species was isolated from 2.5 % of total samples, with three serotypes, Enteritidis, Saintpaul, and Essen, identified. Genetic analysis confirmed the uni versal presence of the invA virulence gene in all Salmonella isolates, while hilA and fimH were detected in 66.6 % and 33.3 %, respectively. In search of sustainable alternatives to synthetic preservatives, this study assessed the antimicrobial properties of cumin oil, rosemary extract, and chitosan. GC-MS analysis identified cuminaldehyde (27.3 %) and 1,8-cineole (25.7 %) as key active constituents in cumin and rosemary, respectively. Preservation trials confirmed the efficacy of all tested agents, with chitosan exhibiting the most potent antimicrobial activi ty—achieving a reduction of 1.5 log 10 CFU/g in Enterococcus and 1.0 log 10 CFU/g in psychrotrophic bacteria after nine days of cold storage—while preserving overall sensory acceptability. These findings support integrating natural antimicrobials into post-harvest fish preservation systems, aligning public health protection with envi ronmentally conscious practices.