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Aquatic microbiology is the science that deals with microscopic living organisms in fresh and salt water systems. Though aquatic microbiology encompasses all microorganisms, including microscopic plants and animals, it refers more commonly to the study of bacteria, actinobacteria, fungi and viruses and their relationships to other organisms in the aquatic environment. Aquatic microbial research embraces a variety of disciplines, ranging from molecular biology and physiology to population dynamics and ecosystem ecology. Aquatic microbes especially in the marine biotopes play a significant role in oceanic processes such as synthesising food, decomposing organic matter, recycling nutrients, and effecting climatic conditions. Although microbes constitute over 90% of oceanic biomass, their biodiversity remains largely unexplored. Microbial diversity and its functions will be significantly affected by critical phenomena such as ocean warming and EI Nino oscillation. Microbial biotechnological approaches and molecular techniques continue to provide us with information on microbes potential for various industrial applications, bio-geographical diversity and phylogeny. There is immense scope for bio-prospecting of aquatic microbes for a wide range of applications. Thus, aquatic microbiology remains instrumental for innovations and future discoveries.