Vibrio parahaemolyticus can cause serious human seafoodborne gastroenteritis and even death. In this study, we isolated and characterized 208 V. parahaemolyticus strains from 10 species of commonly consumed crustaceans and shellfish available in fish markets in Shanghai, People's Republic of China, in 2014. Most of these aquatic species had not been detected previously. The results revealed an extremely low occurrence of pathogenic V. parahaemolyticus carrying the toxin gene trh (1.9%). However, a high level of resistance to the antibiotics ampicillin (94.2%), rifampin (93.3%), and streptomycin (77.9%) was found. Approximately 74.5% of the isolates had multidrug-resistant phenotypes. Tolerance to the heavy metals Cu(2+), Pb(2+), and Cd(2+) was detected in the majority of antibiotic resistant isolates. The resistance patterns differed depending on the tested samples. The crustaceans Penaeus monodon and Marsupenaeus japonicus harbored more antibiotic-resistant bacteria, whereas the isolates from the crustacean Litopenaeus vannamei and the shellfish Busycon canaliculatus had high tolerance to eight heavy metals tested. In contrast to the wide distribution of multidrug resistance and tolerance to heavy metals, lower percentages of plasmid DNA (22.6%) and SXT/R391-like integrative and conjugative elements (4.8%) were detected in the isolates, suggesting that V. parahaemolyticus in these aquatic species may have adopted some other molecular mechanisms that mediated the high prevalence of resistance determinants. The results of this study support the need for food safety risk assessment of aquatic products.