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