Vibrio parahaemolyticusis a seafoodborne pathogen that can cause severe gastroenteritis and septicemia diseases in humans and even death. The emergence of multidrug-resistantV. parahaemolyticusleads to difficulties and rising costs of medical treatment. The bacterium of environmental origins containing no major virulence genes (tdhandtrh) has been reported to be associated with infectious diarrhea disease as well. Identification of risk factors inV. parahaemolyticusis imperative for assuming food safety. In this study, we obtained secretomic and proteomic profiles ofV. parahaemolyticusisolated from 12 species of commonly consumed aquatic products and identified candidate protein spots by using two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry techniques. A total of 11 common and 28 differential extracellular proteins were found from distinct secretomic profiles, including eight virulence-associated proteins: outer membrane channel TolC, maltoporin, elongation factor Tu, enolase, transaldolase, flagellin C, polar flagellin B/D, and superoxide dismutase, as well as five antimicrobial and/or heavy metal resistance-associated ABC transporter proteins. Comparison of proteomic profiles derived from the 12V. parahaemolyticusisolates also revealed five intracellular virulence-related proteins, including aldehyde-alcohol dehydrogenase, outer membrane protein A, alkyl hydroperoxide reductase C, phosphoenolpyruvate-protein phosphotransferase, and phosphoglycerate kinase. Additionally, our data indicated that aquatic product matrices significantly altered proteomic profiles of theV. parahaemolyticusisolates with a number of differentially expressed proteins identified. The results in this study meet the increasing need for novel diagnosis candidates of the leading seafoodborne pathogen worldwide.