- Department of Botany
- Department of Experimental Plant Biology
- Department of Zoology
- Department of Medical Biology
- Department of Ecosystem Biology
- Institute of Physics
- Department of Molecular Biology and Genetics
- Institute of Mathematics
- Department of Parasitology
- Institute of Applied informatics
- Institute of Chemistry
- Language Department
- Czech Arctic Research Station
- Centre for polar ecology
- Laboratory of Archaeobotany and Palaeoecology