The present study aimed to investigate bacterial quality of tilapia fish (Oreochromis niloticus) and evaluate the hygienic health hazard of fish contaminated with some food borne pathogens. Bacteria were isolated from intestine, gills and flesh of Oreochromis niloticus collected from Lake Manzala during two seasons; winter and summer, 2017. Microbiological studies was applied for all samples as total viable bacteria, total coliform, faecal coliform, faecal streptococcus and examined for the presence of Pseudomonas sp. Results show that total viable bacterial count mean was highest in intestine 222 x 104 CFUg-1 in summer. Total coliform count mean was highest in intestine 425 x 103 CFUg-1 in summer. Faecal coliform count mean was highest in gills 90 x 102 CFUg-1 in summer. Faecal streptococcus detected in fish organs only in summer. P. aeruginosa count mean was highest in intestine 185 x 102 CFUg-1 in summer. Molecular identification of suspected colonies was as DNA extraction, PCR technique using ISSR protocol and sequencing, using the nucleotide sequences of the genes for 16S rRNA revealed different strains of Pseudomonas aeruginosa. All isolates were tested for resistance to 10 groups of antibiotics namely Tetracycline (10μg), Gentamicin (10μg), Ampicillin (10μg), Trimethoprim/Sulphamethoxazole (25μg), Vancomycin (30μg), Erythromycin (15μg), Ciprofloxacin (30μg), Chloramphenicol (30μg), Amoxicillin (10μg) and Rifampicin (5μg) using Kirby-Bauer disc diffusion method. The results showed high frequency of multi-drug resistance to many antibiotics, particularly penicillin, ampicillin and chloramphenicol. Therefore this fish species caught from the Lake Manzala may pose health hazards to human and the whole ecosystem.