The Doctoral level may be of particular interest to foreign students. The Ph.D. study fields are shown in the table.
| PhD programme | Programme director | Contact | Co-operating institutions | Guaranteeing department |
| Botany | Assoc. Prof. Jan Kučera | (420)-387772383 kucera@prf.jcu.cz | Institute of Botany AS CR | Department of Botany |
| Entomology | Assoc. Prof. Oldřich Nedvěd | (420)-387772253 nedved@prf.jcu.cz | Biology Centre of AS CR | Departmnet of Zoology |
| Ecosystem Biology | Prof. Hana Šantrůčková | (420)-387772361 hasan@prf.jcu.cz | Biology Centre of AS CR | Department of Ecosystem Biology |
| Hydrobiology | Prof. Jaroslav Vrba | (420)-387772346 jaroslav.vrba@prf.jcu.cz | Biology Centre of AS CR, Institute of Microbiology AV CR | Department of Ecosystem Biology |
| Molecular and Cell Biology and Genetics | Assoc. Prof. Tomáš Doležal | (420)-387772229 dolezt04@prf.jcu.cz | Biology Centre of AS CR, Institute of Animal Physiology and Genetics AS CR | Department of Genetics and Department of Molecular biology |
| Parasitology | Assoc. Prof. Oleg Ditrich | (420)-387776320 oleg@paru.cas.cz | Biology Centre of AS CR | Department of Parasitology |
| Physiology and Developmental Biology – Animal or Plant Specialization | Prof. Dalibor Kodrík Prof. Jiří Šantrůček | (420)-387775271 kodrik@entu.cas.cz (420)-387772353 jsan@prf.jcu.cz | Biology Centre of AS CR Institute of Microbiology AV CR | Department of Animal Physiology and Department of Plant Physiology |
| Biophysics | Prof. Tomáš Polívka | (420) 3807776259 tpolivka@jcu.cz | Biology Centre of AS CR, Global Change Research Centre AS CR | Institute of Physics and Biophysics |
| Zoology | Assoc. Prof. Radim Šumbera | (420)-387772240 sumbera@prf.jcu.cz | Biology Centre of AS CR, Institute of Vertebrate Biology AS CR, Institute of Animal Physiology and Genetics AS CR | Department of Zoology |
| Infection biology | Prof. Jan Kopecký | (420)-387776274 jan@paru.cas.cz | Biology Centre of AS CR | Department of Medical Biology |
| Biochemistry | Prof. Ivana Kutá Smatanová | (420)-387776274 | Department of Chemistry |