Laboratory of Archaeobotany and Palaeoecology (LAPE) is specialized research body of the university founded in September 2002 at the Faculty of Science, University of South Bohemia as part of the Department of Botany. Since 2014 LAPE is a separate department of Faculty of Science.

Research activity of laboratory members is targeted at the area of bioarchaeology and palaeoecology, namely archaeobotany, archaeozoology, but also other specializations dealing with interaction between humans and environment in history. Bachelor, magister and doctor theses namely in botany, zoology and environmental archaeology are developed within the laboratory. In the case of environmental archaeology, laboratory closely collaborates with the Institute of Archaeology of the Faculty of Arts of the University of South Bohemia. LAPE comprises research in the Czech Republic as well as abroad. LAPE also offers services for other research bodies. Besides consultancy concerning natural sciences in archaeology LAPE provides analytical work in several areas of bioarchaeology. LAPE co-edits the international journal Interdisciplinaria Archaeologica, Natural Sciences in Archaeology (IANSA).

Centre for Polar Ecology

The Centre for Polar Ecology aims to promote and facilitate research and education in polar ecological sciences at the  Faculty of Science, University of South Bohemia in České Budějovice. 
CPE offers several courses related to polar ecology. Above all "Polar ecology course" consisting of two components, Life and Earth science. The course itself consists of 1 week intensive theoretical preparation in respective fields of interest and then about 2 weeks of field work on the Josef Svoboda research station in Svalbard.

Center for Mathematical Biology

The Department of Mathematics is responsible for two bachelor study programs Applied mathematics and Mathematics for education, and for the mathematical part of the master study program for those who want to become high school math teachers. The Department of Mathematics offers several unique courses on applications of mathematics in biological and technical sciences. Research focus is mainly on applications of mathematics in biology, on numerical mathematics, and geometry.

The Department offers chemistry studies at bachelor, master and doctoral degree levels and a special education program for secondary schools' chemistry teachers.

Research at the department is closely related to a teaching and students are encouraged to be involved in scientific projects at an early stage of their studies. The research often includes an interdisciplinary scientific work on a border of chemistry and biology, physics or computer science. A very close cooperation with institutes of Biological Center of the ASCR in a shared campus is also beneficial.

The research at the department includes biochemistry, structural biology, environmental and analytical chemistry, computer modeling in chemistry and biochemistry, mass spectrometry, biological research at the level of single molecules and a study of photosynthetic processes.

In addition to the standard study programs, the department also offers programs in cooperation with the Johannes Kepler University in Linz, Austria. It is represented by a cross-border bachelor and master degree programs in Biological Chemistry taught in English in Linz and České Budějovice.

The study of chemistry at the Faculty of Science of the University of South Bohemia offers students a unique opportunity to combine modern chemistry with an excellent research in biology, physics and other disciplines conducted at a progressive institution with a pleasant and friendly environment.