Several species of Vibrio were identified in 4% of total examined samples with the highest isolation in human stool samples. Vibrio cholerae (V. cholerae) was highly isolated in raw milk (66.7%), whereas Vibrio parahaemolyticus (V. parahaemolyticus) was highly isolated in yoghurt (75%) out of the positive samples. The tested cholera toxin (ctxAB), haemolysin toxin (hlyA) and the toxin-coregulated pilus (tcpA) associated-virulence genes were identified in all V. cholera isolates. However, the thermostable direct haemolysin (tdh) and the thermostable direct haemolysin-related haemolysin (trh) associated-virulence genes were identified in 33.3% and 16.7% of the examined V. parahaemolyticus isolates, respectively. The multiple antibiotic resistance (MAR) index ranged from 0.15 to 0.54. Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction showed a higher respective discriminatory power to V. cholerae and V. parahaemolyticus (D = 0.93 and D = 1, respectively) isolates. Lactobacillus rhamnosus (L. rhamnosus) probiotic activity on V. cholerae and V. parahaemolyticus can eliminate or significantly reduce the number of bacteria. In conclusion, most V. cholerae and V. parahaemolyticus isolates exhibited resistance to multiple antimicrobial classes. However, tetracycline, trimethoprim–sulfamethoxazole, chloramphenicol, and meropenem were recommended to treat vibriosis. L. rhamnosus could be used as an effective and applicable method for controlling antimicrobial-resistant Vibrio isolates.