In spring of 1929 the Black Sea Hidrophysical Station was founded at the initiative of academician Vladimir Shuleykin at the Southern Coast of the Crimea in Katsiveli village. Its main mission was to carry out complex research of the processes in the sea coastal area.

Marine Hidrophysical Institute of Academy of Sciences of the USSR was created in 1948 in Moscow on the basis of the Black Sea Hidrophysical Station of Academy of Sciences of the USSR and Marine Hidrophysical Laborarory (formerly, the department of the Institute of Theoretical Geophysics of Academy of Sciences of the USSR). Vladimir Shuleykin (1895 – 1979), the foremost scientist-oceanographer became its director.

The first scientific achievements of Marine Hydrophysical Institute (MHI) are related to studies of thermal phenomena in the ocean, thermal interaction between the oceans, the atmosphere and continents and also the World Ocean impact on climate and weather. Immediate observations of storm waves at the Black Sea Hydrophysical Station and their modeling in the storm basin created the physical foundations of the theory of sea waves. A large number of experimental and theoretical works in the field of marine environment optics and biophysics were published. The results of the studies were summarized by Vasiliy Shuleykin in the unique monograph "Physics of the Sea", awarded the USSR State Prize (1942).

In August, 1961 MHI entered the system of Academy of Sciences of Ukrainian SSR. In 1963 the Institute was relocated to Sevastopol. Arkadiy Kolesnikov (1907 – 1978), the academician of Academy of Sciences of Ukrainian SSR, became its Director.

In Sevastopol the Institute was actually new created. It rushed in the Soviet and world ocean science, having become a recognized authority in the study of physical processes in the World Ocean, the automation of oceanographic research and marine instrumentation. The most significant result of this period was the discovery, experimental and theoretical study of the equatorial countercurrent in the Tropical Atlantic, named after Mikhail Lomonosov. In 1970, a group of MHI scientists (С. Boguslavskiy, G. Grigor'ev, Arkadiy Kolesnikov, G. Ponomarenko, Artyom Sarkisyan, A. Felzenbaum, N. Khanaichenko) was awarded the USSR State Prize for this discovery.

In 1974 – 1985 the Head of MHI was Boris Nelepo (1932 – 2007), the academician of Academy of Sciences of Ukrainian SSR. During this period, the scientists of the Institute studied the patterns of the ocean climate formation and its interaction with the atmosphere, the tropical water circulation, mesoscale and synoptic variability of hydrophysical fields, their fine structure and the dynamics of surface and internal gravitational waves. The research in the field of hydrooptics, nuclear and physical chemistry of the sea was also carried out. The works of the physical and technical profile were intensively developing. They were aimed at creating new measuring complexes for the World Ocean research. Boris Nelepo was the founder of satellite hydrophysics, the new scientific field of the MHI research, being still one of the main ones in the Institute to the present days.

In these years, with the use of oceanographic satellites, the first large-scale long-term experiments in the World Ocean were carried out. They formed the basis of a scientific field unique for its information opportunities. For a series of studies in the field of satellite hydrophysics, Boris Nelepo and Yuriy Terekhin were awarded the USSR State Prize (1989).

In 1985 the academician of the National Academy of Sciences of Ukraine Valeriy Eremeev became the Director of MHI. In these years MHI significantly strengthen the works of ecological and oceanographic focus, the research on the complex dynamics of marine systems, satellite hydrophysics, numerical modeling of marine environment dynamics, information support of the World Ocean studies.

Since April 2000 the duties of the Director of MHI were performed by Vitaliy Ivanov, the academician of the National Academy of Sciences of Ukraine (since 2010 the Director of MHI). Under the leadership of Vitaliy Ivanov MHI developed the research of marine shelf zones under conditions of anthropogenic and technogenic loads for solving the problems of optimal planning of a particular natural region development and performing the most economically feasible use of all types of shelf resources simultaneously with the improvement of the ecological state of the marine environment. In this period under the guidance of Gennadiy Korotaev, corresponding member of the National Academy of Sciences of Ukraine, MHI specialists actively participated in the development of the operational observation and forecasting system of the marine environment state (operational oceanography) at all stages: from the implementation of the ocean satellite monitoring concept to the creation of a system for nowcast/forercast of 3D fields of the Black Sea currents, temperature and salinity. MHI was not just the active participant of main European programs in the field of operational oceanography but also the only regional center of the Black Sea marine environment operative forecast.

After the formation of two new constituent entities (the Republic of Crimea and the city of federal status Sevastopol) within the Russian Federation, Marine Hidrophysical Institute of the National Academy of Sciences of Ukraine was renamed Federal State Budget Scientific Institution “Marine Hidrophysical Institute of RAS” (FSBSI MHI) according to Sevastopol Government decision of February 24, 2015 and was headed by corresponding member of the National Academy of Sciences of Ukraine Gennadiy Korotaev. Due to the efforts of administration and personnel of the institute as well as the help from scientific and civil society, the institute and its material and technical base were preserved during this period. Federal State Budget Scientific Institution “Marine Hidrophysical Institute of RAS” (FSBSI MHI) was created by a resolution of the Government of the Russian Federation of April 9, 2015 and headed by corresponding member of Russian Academy of Sciences Sergey Konovalov.

In 2019, the institute celebrated its 90 year anniversary. A significant event of this year became the unification of Marine Hydrophysical Institute with the Black Sea Hydrophysical Polygon (based in Katsiveli). The Institute received the status of the Federal Research Center. Now its full formal name is: Federal State Budgetary Scientific Institution Federal Research Center “Marine Hydrophysical Institute of the Russian Academy of Sciences” (abbreviated as FSBSI FRC MHI)

At the present time FSBSI MHI continues the scientific traditions of fundamental research of seas and oceans established at the previous stages of its history. New fields related to geo-information technologies, regional studies and innovative instrument-making are also developing.