Food microbiology has been revolutionized by the advances in molecular genetic technology of microbial ecology.Novel microbial detection methods have been applied in the study of processing and storage of aquatic food products.The microbial diversity in the sample to be studied could be detected by high-throughput sequencing(HTS)approaches as culture-independent analyses.The aim of this review is to give a brief introduction of the microbial amplicon HTS technology,to present a survey of recent aquatic food investigations via 16 S rRNA amplicon HTS and to illustrate the potential of this approach for a valuable tool in the better characterization of aquatic foods and their processing and storage.