Marine microorganisms are defined by their habitat as microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism (or microbe) is any microscopic living organism or virus, which is invisibly small to the unaided human eye without magnification. Microorganisms are very diverse. They can be single-celled or multicellular and include bacteria, archaea, viruses, and most protozoa, as well as some fungi, algae, and animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify viruses as microorganisms, but others consider these as non-living.

Marine microorganisms have been variously estimated to make up between 70 and 90 percent of the biomass in the ocean. Taken together they form the marine microbiome. Over billions of years this microbiome has evolved many life styles and adaptations and come to participate in the global cycling of almost all chemical elements. Microorganisms are crucial to nutrient recycling in ecosystems as they act as decomposers. They are also responsible for nearly all photosynthesis that occurs in the ocean, as well as the cycling of carbon, nitrogen, phosphorus and other nutrients and trace elements. Marine microorganisms sequester large amounts of carbon and produce much of the world's oxygen.

A small proportion of marine microorganisms are pathogenic, causing disease and even death in marine plants and animals. However marine microorganisms recycle the major chemical elements, both producing and consuming about half of all organic matter generated on the planet every year. As inhabitants of the largest environment on Earth, microbial marine systems drive changes in every global system.

In July 2016, scientists reported identifying a set of 355 genes from the last universal common ancestor (LUCA) of all life on the planet, including the marine microorganisms. Despite its diversity, microscopic life in the oceans is still poorly understood. For example, the role of viruses in marine ecosystems has barely been explored even in the beginning of the 21st century.

Marine microorganisms have been variously estimated to make up about 70%, or about 90%, of the biomass in the ocean. A microorganism, or microbe, is a microscopic organism too small to be recognised adequately with the naked eye. In practice, that includes organisms smaller than about 0.1 mm.

Such organisms can be single-celled or multicellular. Microorganisms are diverse and include all bacteria and archaea, most protists including algae, protozoa and fungal-like protists, as well as certain microscopic animals such as rotifers. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify viruses as microorganisms, but others consider these as non-living.

Microorganisms are crucial to nutrient recycling in ecosystems as they act as decomposers. Some microorganisms are pathogenic, causing disease and even death in plants and animals. As inhabitants of the largest environment on Earth, microbial marine systems drive changes in every global system. Microbes are responsible for virtually all the photosynthesis that occurs in the ocean, as well as the cycling of carbon, nitrogen, phosphorus and other nutrients and trace elements.

While recent technological developments and scientific discoveries have been substantial, we still lack a major understanding at all levels of the basic ecological questions in relation to the microorganisms in our seas and oceans. These fundamental questions are:
1. What is out there? Which microorganisms are present in our seas and oceans and in what numbers do they occur?
2. What are they doing? What functions do each of these microorganisms perform in the marine environment and how do they contribute to the global cycles of energy and matter?
3. What are the factors that determine the presence or absence of a microorganism and how do they influence biodiversity and function and vice versa?