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Located in Ceske Budejovice, better known abroad for its tradition of brewing under the Habsburg-era name of Budweis, the University of South Bohemia was founded in 1991 by the merger of local faculties of education, dating to 1948, and agriculture, formed in 1960.

The faculties of biology, theology, social sciences and health were added at the time of foundation, followed by arts, economics and fisheries and water protection in the first decade of the present century.

It defines itself as "A research university focussing mainly on natural science, social science and humanities" and in 2018 it offered 228 undergraduate majors including 30 options in English and three in German.

The study of biology, aided by the presence of the Czech Academy of Science’s national research institute in the city, is a particular strength. A degree in biological chemistry has been offered in partnership with the University of Linz, Austria since 2007.

Ranked seventh for research among Czech universities in the 2019 Nature Index, the university has specialist laboratories focussed on ant ecology, with extensive research in Borneo and Papua New Guinea, and on archaeobotany and palaeocology.

The Centre for Polar Ecology is an affiliate of the University of the Arctic Network. Water scientists have developed a new species of carp and assisted local industry by using crayfish to analyse the quality of water used in brewing.

Campus architects have aimed to create an "English-style park" whose features include the Czech Republic’s second "Havel’s Place" feature, a table and chairs laid out for conversation in memory of the playwright-turned-President.

Alumni include Hynek Kmomicek, Czech ambassador to the USA, who took a master's in classical guitar and education.