The study on marine microbial diversity is highly valuable and promising, and will greatly improve the exploitation and utilization of microbial resources. Since the vast majority of marine microbe are unculturable, the molecular biology becomes the main way in the study of marine microbial diversity. Recently, the research strategy and technology developes fast, and this paper summarized the researches of marine microbial diversity based on molecular biology and compared different research methods. Besides, it envisioned the future of marine microbial diversity study based on the progress of this field and molecular ecology technology. This paper is valuable for the further study on marine microbial diversity as well as the ex-ploitation and utilization of marine microbial resource.