Vibrio parahaemolyticus is one of the most hazardous pathogens causing seafood-borne diseases in the southern Fujian coast, China. From June to October 2016, a total of 250 samples were collected from retail markets in the Xiamen, Quanzhou, and Zhangzhou regions. Seventy-seven V. parahaemolyticus isolates were identified using polymerase chain reaction (PCR). Then, molecular typing was performed using repetitive extragenic palindromic-PCR (REP-PCR). The distribution of seven virulence genes was detected by PCR. In aquatic products, the prevalence of V. parahaemolyticus was 30.8%, and the prevalence of tdh + and trh + was 2.6 and 1.3%, respectively. The prevalence of type III secretion system-2 (T3SS2) and the ureC gene was 5.2 and 3.9%, respectively. All 77 strains and the reference strain V. parahaemolyticus ATCC 17802 were classified into seven molecular types using REP-PCR. Thus, our findings demonstrated that the prevalence of V. parahaemolyticus was severe in the southern Fujian coast and that the regulations for aquatic food safety should be strengthened. 1 | INTRODUCTION Vibrio parahaemolyticus (V. parahaemolyticus) is a Gram-negative, halophilic, rod-shaped bacterium that is commonly found in aquatic products in China, Japan, Korea, and other countries with long coastlines. The germ load of V. parahaemolyticus in the environment is inclined to follow clear seasonal trends, with food-borne diseases peaking in the summer months (Chen et al., 2017; Paranjpye et al., 2015). The consumption of contaminated aquatic products in the aquaculture sector is very high, which gives rise to the high prevalence of gastroenteritis infections caused by V. parahaemolyticus during summer and autumn. This food-borne pathogen can infect people through the consumption of raw or undercooked aquatic animals, especially fish, mollusks, crustaceans, etc. (Xie, Wu, Zhang, Xu, & Cheng, 2016). Patients infected with V. parahaemolyticus are most likely to experience diarrhea, abdominal cramps, vomiting and fever, septicemia, or even death (Lopatek, Wieczorek, & Osek, 2015). The number of food poisoning cases caused by V. parahaemolyticus has exceeded that caused by Salmonella, ranking first in food-borne pathogens in China (Broberg, Calder, & Orth, 2011). In recent years, several reports concerning the prevalence of V. parahaemolyticus in seafood or environmental samples have been delivered in many coastal areas in China. In seafood samples, the prevalence of V. parahaemolyticus was reported to be 10% in Zhejiang Province (Chen et al., 2017),