Pathogenic Vibrios have emerged as a serious and global threat to human health. Of particular concern are Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae, which cause diarrhea, gastroenteritis and septicemia. Of increased concern is the expanding range of detection in areas not naturally endemic to pathogenic Vibrio species, i.e., northern temperate and colder climates. The purpose of this study was to combine culture-based detection with molecular typing methods to identify what pathogenic Vibrio species are present in the Great Bay Estuary, NH and to determine their virulence potential. V. parahaemolyticus, V. vulnificus, and, for the first time, V. cholerae, were all identified from oyster, water and sediment samples during 2007-08, though no isolates contained clinical/human virulence genes. V. parahaemolyticus was detected most frequently, all Vibrio were more abundant in oysters and sediments than in water, and V. cholerae was rarest. V. parahaemolyticus abundance was most associated with temperature because of wide seasonal differences during the study, but did not vary among sample sites despite varying environmental conditions. The threat of human vibrio infections in the Gulf of Maine from exposure to shellfish and coastal waters under expected global warming conditions is a growing concern.