The Institute of Ecology and Geography established in accordance with the Decision of the Government of the Republic of Moldova "On measures to optimize the infrastructure of science and innovation" No. 1326 of December 14, 2005 by merging the National Institute of Ecology of the Ministry of Ecology and Natural Resources and the Institute of Geography of the Academy of Science of Moldova.

The development of geographical science in the Republic of Moldova began in 1946, when the Sector of Economics and Geography was created as part of the Moldovan Base of Scientific Research of the U.R.S.S Academy of Sciences. In 1950, it was transformed into the Geography and Cartography Sector within the Economics Sector (since 1960 - Institute of Economics) of the Moldovan Branch of the U.R.S.S. Academy of Sciences. In 1965, on the basis of this sector was created the Geography Section of the Academy of Sciences of the Soviet Socialist Republic of Moldova, which taking into account the timeliness, practical and theoretical importance of research, the scientific potential, so  in 1992 was awarded the status of Geography Institute of the Academy of Sciences of Moldova.

The National Institute of Ecology was established in 1990 on the basis of the Science, Monitoring and Ecological Norms Department of the Department of Environmental Protection; Forestry and Experimental Resort with the experimental forest district Hârbovăţ; the technological and design center, the scientific sections of the "Codru" and "Iagorlâc" reservations; the Plant protection section from Straseni and the pedological resort from Bender. Since 1992, the Institute has been under a double subordination: of the Department of Environmental Protection (later - Ministry of Ecology and Natural Resources) and, methodically - of the Academy of Sciences of Moldova.

The main contribution in the development of the Institute of Geography belongs to m.c. M. Radul, Dr. in Geographical Sciences V. Proca, Dr.hab. A. Levadniuc, academics Tatiana Constantinov and A. Ursu, the m.c., prof., Maria Nedealcov, and of the National Institute of Ecology - the m.c., prof., I. Dediu, who was its founder.