The paper analyzes methodological foundations for selection of educational content about the structure and life of protozoa in the university course Zoology while training bachelors of Pedagogical education majoring in Biology and Chemistry. The authors test the hypothesis that the methodological foundations of the study of protozoa are the achievements of biological sciences, as well as formulated methodological constructs based on the recognition of ecological and evolutionary approaches. General scientific methods of theoretical knowledge as well as methods used at the empirical and theoretical levels of knowledge were used as research methods. The methodological foundations for selecting the educational content about the structure and life of protozoa in the university course Zoology are: general properties of living organisms, levels of life organization, ideas of development and structure, an ecological-evolutionary approach, description of co-evolutionary processes and the role of cognitive models. The belonging of unicellular organisms to the cellular level of life organization does not prevent their description taking into account the structural-functional approach with the substantiation of a close connection between the vital processes of unicellular and multicellular organisms. Methodological attitudes operating in biological knowledge are associated with an orientation towards the idea of development and organization. The study of unicellular organisms biology taking into account the above ideas is guided by ecological and evolutionary aspects. The formulated approach is important from a practical and theoretical point of view. The aspects of the practical application of knowledge about the biology of protozoa include, for example, the study of their role in the life of the biosphere. Evolutionary aspects in the description of protozoa are realized at the phylogenetic and ontogenetic levels.