The present study was designed to determine the prevalence of Vibrio and Aeromonas in Nile tilapia and Mugil fish farms in Egypt and monitoring some virulence genes associated with V. parahaemolyticus and A. hydrophila isolates. One hundred diseased fishes (50 for each Nile tilapia and Mullet fish) were collected over 10 months from January to October 2019 and submitted to bacteriological and biochemical examination. Randomly selected 5 isolates of Vibrio species were submitted for molecular identification using species-specific PCR (toxR gene for V. parahaemolyticus and collagenase for V. alginolyticus) and the molecular detection of virulence genes including recA and trh in V. parahaemolyticus isolates. Other 5 A. hydrophila isolates were examined for the molecular detection of virulence genes including fla, aerA, hlyA, and ahcytoen genes. Vibrio species isolated with a prevalence of 65.0% for 100 examined fishes. Vibrio parahaemolyticus, V. alginolyticus, and V. cholerae were isolated with a prevalence of 55.4, 33.8, and 10.8%, respectively. Aeromonas species were isolated with a prevalence of 72.0% for 100 examined fishes where A. hydrophila and A. caviae were isolated with a prevalence of 99.3 and 9.7%, respectively. PCR results showed toxR gene was detected in all five isolated Vibrio species, recA virulence gene was detected in three out of the five tested V. parahaemolyticus isolates. Meanwhile, the trh gene was not detected. On the other hand, aerA and hlyA virulence genes were detected in all five isolated A. hydrophila. Ahcytoen was detected in 4 out of 5. Meanwhile, the fla gene was detected in 1 out of the tested 5