Vibrio parahaemolyticus and Vibrio vulnificus are pathogenic microorganisms belonging to the Vibrionaceae family and the genus Vibrio. They are microorganisms with morphology curved, gram negative and oxidase positive. Regarding environmental aspects, both species are halophilic, so often present in coastal marine waters and within molluscs, crustaceans and fish, and they are usually found in warm waters. The pathology is produced by consumption of seafood, shellfish and raw or undercooked fish and exposure to contaminated water. Both species are considered emerging pathogens due to the increase in incidence and geographic distribution of most food poisoning cases, especially in Asian countries. The detection and identification of both species in seafood and water, has high difficulty, since the conventional methods are long and tedious, and can provide false negatives. Molecular detection methods can make a faster alternative, sensitive and reliable. Because of this, in this work we have developed methods of detection and quantification of Vibrio spp., Vibrio parahaemolyticus and Vibrio vulnificus by traditional PCR, real-time PCR and in situ hybridization with fluorescent probes (FISH) for use in food samples and in water. The results show that real-time PCR is more rapid and sensitive method for detecting the different species studied, and allows the quantification of microorganisms in samples reliably. In this study, various methods have been applied to environmental samples (beach water and waste water) and seafood. In this study, we demonstrated the presence of Vibrio bacteria in both types of samples and potential water and seafood to act as vehicles for transmission of V. parahaemolyticus and V. vulnificus. Our results on the presence of these pathogens in both types of samples are relevant enough to consider that V. parahaemolyticus and V. vulnificus may pose a risk to human health in our geographic area.