The land and building of the present Institute of Ecology and Botany were bequeathed by Count Sándor Vigyázó to the Hungarian Academy of Sciences in 1919. This ownership was the basis of the foundation of the Institute. The estate at Vácrátót consisted of a manor house, farm buildings and a 20 ha park created around 1830. After the devastation of the Second World War, the property got into the possession of the Natural History Museum. The Course on Geobotany and Vegetation Mapping organized here in the summer of 1949 and 1950 was a milestone for the development of phytosociology.

In 1952, when the Academy was reorganized and the network of academic institutions was established, the Nature Conservation Park and Biological Station of Vácrátót became part of the administration of the Academy and the Research Institute for Botany of the Hungarian Academy of Sciences was founded. The first director of the Institute was Gábor Szemes, and Antal Pénzes laid the foundations of the Botanical Garden. A Scientific Committee, consisting mainly of experts of other institutes, was appointed for the co-ordination of scientific tasks.

The president of the Academy appointed Bálint Zólyomi as director in 1954. Miklós Ujvárosi who directed the Botanical Garden became deputy director at the same time. After a decade of collecting and reconstruction work, the Botanical Garden owned the largest collection of living plants in Hungary, in addition, a unique collection of plants arranged according to a phylogenetic system was established. New glasshouses were built in the 1960s. The huge gene collection of the Garden was a reliable source and reserve of propagation material in the past decades for applied botanical studies in Hungary. The Garden also plays an important role in nature conservation education.

The Institute originally consisted of three sections: the Botanical Garden, the Department of Plant Physiology and the Department of Geobotany. The Department of Plant Physiology existed for only a short period. Geobotanical research followed the general directions laid down by the Course on Geobotany and Vegetation Mapping of the year 1950. Description and mapping of various Hungarian landscapes were accomplished following the classical coenological methodology of Braun-Blanquet. A slightly different direction was represented by the study of segetal weeds. A successful symposium, the International Geobotanical Symposium, on the vegetation of the Carpathians organized by the Institute in 1967 can be considered as the completion of this period.

The Institute joined the International Biological Program (IBP) in the second half of the 1960s by the decision of the management. Studies on the production biology of alkaline steppe communities and salt-effected cultivated vegetation stands started. Regular sampling by standardized methods have been performed for several years to assess phytomass production. In addition, studies on climatology, pedology and zoology were carried out and statistical methods were introduced for the evaluation of data. A research station for field studies was established for the first time in Hungary, and individual research was replaced by team work. The Institute co-ordinated the International Biological Program terrestrial productivity research that took place in the country.

From the beginnings of the 1970s, four thematic research teams were formed in the Department of Plant Ecology (formerly Department of Geobotany), namely the teams of Phytocoenology, Soil Ecology, Quantitative Ecology and Production Ecology. Researchers belonging to the latter had studied the phytomass at the IBP station first, and started the chemical and ecological investigations of the active ingredients of medical plants from the early 1970s. The Botanical Garden contributed considerably to these investigations with its potential and experience in the cultivation of plants.

The Presidency of the Academy decided to restructure and extend the activities of the Institute in 1977. The Hungarian Danube Research Station that was established in 1957 and functioned as a research team of Eötvös Loránd University joined the Institute as a department, but keeping its former name. The basic aims of Danube research were defined by the International Working Panel of Danube Research: baseline survey of the river according to standardized methods as well as principles, and revealing the ecological processes and hydrological and biological interactions.

After the retirement of Bálint Zólyomi and Miklós Ujvárosi, a new governing body was nominated. Árpád Berczik, the previous head of the Danube Research Station, was appointed as director, Attila Borhidi became deputy director. New national and international tasks were added to the activities of the Hungarian Danube Research Station (e.g. Fertő Lake Biosphere Reserve Program according to the agreement between UNESCO and the Academies of Hungary and Austria). Other international programs enriched the international connections of the Institute (e.g. the Zapata Project in Cuba, and the Usambara Rain Forest Project in Swedish-Hungarian-Tanzanian co-operation). Urban ecological research started when the ecological investigations of the Budapest Agglomeration were launched in the framework of the Man and Biosphere (MAB) program. Urban ecology studies amplified considerably the methodological repertoire of the Institute.

The changes in the research objectives demanded a change of name of the Institute, since 1984 it is called the Institute of Ecology and Botany of the Hungarian Academy of Sciences. In the same decade, relevant international symposia were organized almost every year. Some examples: the International Bryological Congress (1985), the 24th Conference of the International Working Panel of Danube Research in the same year (the following one in the organization of the Institute was the 31st meeting in 1996), UNESCO-conferences on Lake Fertő (1985, 1987), and the Symposium of the International Association of Botanical Gardens (1989).

In these years, the Botanical Garden became the leading institute of tropical botany and phytotaxonomy in Hungary and gained international reputation in these fields. The taxonomic description and the Red Book of the Cuban flora, the catalogue of African mosses, and the evaluation of the water budget of tropical cloud forests are the result of the intensive work that took place.

The establishment of the Experimental Ecological Research Team indicated changes in research topics: studies on population ecology were launched, investigations on the ecophysiology of plant populations were conducted for a better understanding of vegetation phenomena. A visible sign of the biosphere crisis is the transformation, degradation of vegetation so in Hungary as elsewhere. This is one reason why the description of static vegetation states lost its importance and the study of dynamic processes came to the front. Theoretical questions of vegetation dynamics gained importance, and ? parallel to international trends ? the Institute established permanent plots suitable for long-term monitoring and experimental studies under the guidance of the Head of the Department of Plant Ecology, Gábor Fekete. The members of the staff developed new microcoenological sampling techniques together with computer simulation models. Databases were constructed for handling the huge mass of collected data. Landscape history studies began and expanded in the 1990s. The international reputation of the work is reflected by the fact that the Institute, namely the Experimental Ecology Research Team was entrusted with the organization of the highly successful symposium Mechanisms in Vegetation Dynamics of the International Association for Vegetation Science (IAVS) in 1991.

The Research Team for Production of Chemical Constituents became a permanent, stable group when the National Biological Program terminated. In the first period, tasks included the investigation of the active ingredients of native and cultivable plants of possible economic benefits and the impact of geographical distribution and habitat on the chemical content. Topics focused on more specific objectives later, e.g. the steroid content of native and cultivable plants of possible industrial use was analyzed in the early 1970s. New opportunities opened, the technical background was improved and a better co-operation was achieved when the head of the Research Team, Imre Máthé, was appointed as full professor and head of institute at the University of Szeged keeping his position as leader of his research group in Vácrátót.

In the second half of the 1970s, the long-term research of the Danube focused on the indication of ecological changes in the Hungarian stretch of the Danube. Organic matter content, oxygen budget and trophity, population changes of freshwater organisms in relation with self-purification and human impacts, heavy metal contamination in the water, in the suspended matter, in the phyto- and zooplankton, and in the benthic and periphytic organisms were studied. Impact assessment of the Bős river barrage system was investigated from the 1980s. Studies analyzing the ecological role of reed, including nature conservation aspects, were also important. Taxonomic revision of Diatomes based on the use of electron microscope was improved and enriched by the DNA analysis of pure cultures. These studies were performed in collaboration with the Department of Microbiology of Eötvös Loránd University.

The first half of the 1990s was the period of social and economical transition in the country. The Institute struggled for survival in that time. Staff number was decreased by 40%, researchers had to finance their research and to maintain the Institute at the same time (20 researchers worked in 36 parallel projects). There was hardly any opportunity for comprehensive, extended studies. Efforts were made for acquiring assignments in applied studies, mainly in the fields of nature conservation and environmental protection. Biodiversity (on different levels of organization), its conservation and monitoring gained greater and greater interest. By that time the Institute (and the scientific policy makers) became aware of the fact that the investigation of irreplaceable natural values of Hungary (through mapping, publishing and interpretation of data, construction of databases accessible for information systems) and the study of scientific problems underlying global environmental crisis are of equal importance. The fulfillment of national tasks and the investigation of more general ecological problems of international importance were carried out in parallel. The increasing number of international programs and projects demanded a deep knowledge of local-regional biodiversity (including the characteristic ecosystems and processes). An example to cite is the Long Term Ecological Research program constituting a stable basis for a long-term co-operation with several institutes of the United States and all over Europe.

The consolidation of the Hungarian Academy of Sciences started in 1997, and in this framework ecological research received a special subsidy from the Presidency of the Academy and the Ministry of Environment and Regional Policy. The Institute could improve the infrastructure and could create new positions. Beside the consolidation, the Strategic Research Program of the Hungarian Academy of Sciences has financed the main ecological research topics for three years through a grant system. The Institute has been integrated more and more into international research programs. This fact is reflected in a number of tenders granted by the Framework Programs of the European Union and other organizations like the Food and Agriculture Organization of the United Nations. The Institute was responsible for the development of the International Long Term Ecological Research Network (ILTER) and the Global Terrestrial Observing System (GTOS) for the Central and Eastern European region. The professional staff of the Institute played an important role in the Networking On Long Term Integrated Monitoring in Terrestrial Systems (NoLimits) project as well. The experts of the Institute intensely participated in the establishment of the European Chapter of the Society for Ecological Restoration (SER) too.