Vibrio parahaemolyticus is prevalent in tropical marine environment in all seasons and can cause seafood-borne gastroenteritis. A total of 251 suspected isolates were tested including 60 from frozen shrimp, 50 from cultured live shrimp, 67 from sediments of culture ponds and 74 from water were subjected to polymerase chain reaction (PCR) targeting the toxR gene for confirmation as V. parahaemolyticus. Of the 128 toxR positive isolates, 15% of the isolates from culture environment (from live shrimp, sediments and water) and 7% of frozen shrimp samples were positive for the tdh and trh genes. Since urease production could be a marker of trh but not tdh in V. parahaemolyticus, a total of 189 of the 251 suspected V. parahaemolyticus isolates were tested for urease production and 41% of the isolates were found to be positive for urease production. However not all urease positive strains of V. parahaemolyticus were positive for either tdh or trh genes. Detection of virulent strains in shrimp culture environment in Malaysia suggests a probable risk for health of people consuming raw shrimp.