Estonian Marine Institute was established on the 3 of March in 1992 from the units of Estonian Fishery Institude, Estonian Academy of Sciences Ecology and Marine Research Institute.

In 1996 Estonian Marine Institute was merged with the Ministry of Environment and it was incorporated with University of Tartu in 2001. Estonian Marine Institute has been one of the Faculty of Science and Technology’s research and development institutes since 2008 (earlier it belonged under Faculty of Biology and Geography).

Estonian Marine Institute primarily focuses on the research of the ecosystem and functioning of Baltic Sea, evaluation and prognoses of the marine organisms and environment. It also concentrates to protect the biological diversity of marine life in different ways in Baltic Sea.
Estonian Marine Institute is co-operating with several international organizations. Since 2004, when Estonia became the member of International Council for the Exploration of the Sea (ICES), Estonian Marine Institute carries out several projects, which are co-ordinated by ICES. In addition, Estonian Marine Institute is involved with HELCOM, Baltic Marine Biologists (BMB) etc.