is a waterborne bacterium and can cause epidemic cholera disease worldwide. Continuous monitoring of contamination in aquatic products is imperative for assuring food safety. In this study, we determined virulence, antimicrobial susceptibility, heavy metal tolerance, and genomic fingerprints of 370 isolates recovered from 12 species of commonly consumed aquatic products collected from July to September of 2018 in Shanghai, China. Among the species, , , , and were for the first time detected for . Toxin genes , , , and were absent from all the isolates. However, high occurrence of virulence-associated genes was detected, such as (82.7%), (81.4%), (81.4%, 24.3%, 80.3%, and 80.8%, respectively), and (80.5%). Approximately 62.2% of the 370 isolates exhibited resistance to streptomycin, followed by ampicillin (60.3%), rifampicin (53.8%), trimethoprim (38.4%), and sulfamethoxazole-trimethoprim (37.0%). Moreover, ∼57.6% of the isolates showed multidrug resistant phenotypes with 57 resistance profiles, which was significantly different among the 12 species (multiple antimicrobial resistance index,  < 0.001). Meanwhile, high incidence of tolerance to heavy metals Hg (69.5%), Ni (32.4%), and Cd (30.8%) was observed among the isolates. The enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR)-based fingerprinting profiles classified the 370 isolates into 239 different ERIC-genotypes, which demonstrated diverse genomic variation among the isolates. Overall, the results in this study meet the increasing need of food safety risk assessment of aquatic products.