Pollution of the aquaculture environment has been a serious problem for the future development of aquaculture industry. Because of the significant importance of microorganisms in the environment of aquaculture, this paper provides an overview of modern microbial recognition technology from the technical aspects. According to the targets, the microbial recognition technology was divided into two types: one targetting nucleotides of microorgansims, the other targetting the surface antigens of microorganisms. The application of the two technologies was also summarized in the present paper, which could provide a reference for the improvement of aquaculture environment and the control of the disease in the aquaculture animals.