After successfully completing his/her studies the graduate is able to:

• perform independent or team botanical research at the level of individual plants, populations, species or plant communities
• design sampling strategy, organize field and laboratory experiments and organize field expeditions
• determine common species of algae, fungi, lichens, bryophytes and most of species of vascular plants in Central Europe
• apply theoretical knowledge in plant evolution and ecology to design case studies in botany and nature protection
• select relevant analytical methods, including statistical, and correctly interpret results of ecological, phylogenetic and evolutionary studies

Graduates have knowledge and skills to be able to perform basic and applied research or teaching at biological departments of universities, basic and applied research at biological institutes of the Czech Academy of Sciences, at state or private institutions of nature conservation and environmental protection (e.g., Nature Conservation Agency of the Czech Republic, National Parks, Protected Landscape Areas), at departments of natural history museums, botanical gardens, forest and agricultural research institutes and at comparable institutions abroad.

The standard duration of studies is four semesters. To be admitted to the final state examination, students must obtain a total of 120 ECTS credits for required, selective and elective courses. Required courses constitute the basis of the discipline and make up 62 credits for the specializations of Plant Biosystematics and Plant Ecology and 54 credits for the specialization of Phycology and Mycology (including credits for a Master’s thesis). Students choose selective courses according to their interests and intended professional specialization. The number of credits for selective courses is at least 26 for Plant Biosystematics and Plant Ecology students and 34 for Phycology and Mycology students. The remaining 32 credits can be obtained from elective courses offered in the curriculum of the given study programme or from other courses offered by any other study programme.

For all students, there is an obligation to complete those fieldwork courses from the list which they did not completed during their Bachelor's programme: Bi6631 Floristic Summer School of the Czech Botanical Society, Bi6661 Field Course of Geobotany, Bi6671 Field Course of Czech Flora, Bi6691 Foreign Botanical Excursion.

During the course of their studies, students should follow the Study Catalogue for their year of matriculation. They can access the Study Catalogues through the faculty website.

Even though practical training is not an obligatory part of the study plan, most of the diploma theses are inherently practical and they are carried out in cooperation with the institutes of the Czech Academy of Sciences and Nature Conservation Agency of the Czech Republic.

The final state examination is oral and takes place before an examination board composed of at least 5 members. Based on their specialization, students are examined in four of these five subject areas: (1) System and Evolution of Cyanobacteria, Algae and Fungi, (2) Phylogeny and Diversity of Higher Plants, (3) Plant Ecology and Geobotany (4) Regional Botany, and (5) Methods of Botany, i.e., students of the specialization of Plant Biosystematics and Plant Ecology in the subjects (2–5) and students of Phycology and Mycology in (1), (3–5). Besides their knowledge, the board evaluates the applicant's ability to think independently to analyse and discuss assigned botanical topics. An integral part of the final state examination is also the defence of the Master' thesis.

After completion of the Master's study programme, it is possible to continue further studies in any doctoral study programme (after satisfying the admission requirements). At the Faculty of Science, students can particularly apply for admission to doctoral study programmes of Botany and Ecology.