Background: Saponins are secondary metabolites in plants that play an important role in defense mechanisms and physiological processes. Since stomatal cells are crucial for gas exchange and water balance in plant tissues, studying the anatomical and biochemical features of stomatal cells in saponin-rich plant species provides insight into the interactions between these compounds and cellular mechanisms. This serves as the basis of our study. Aim: To determine the structure, types, and functions of stomatal cells in saponin-containing medicinal plants Materials and Methods: During June–September 2024, nine species of saponin-containing medicinal plants were collected from Bulgan, Tuv provinces, and “Gorkhi-Terelj National Park” in Mongolia. Prepared microscopic specimens were examined using macroscopic and microscopic techniques to study the structure, position, number, and epidermal features of stomatal cells. Results: The study revealed that Anemone crinita Juz. exhibited the highest stomatal density (107 stomata/mm²) and epidermal cell density (229 cells/mm²), indicating strong adaptation and protective capacity in arid conditions. Vicia baicalensis (Turcz.) B. Fedtsch. showed the highest stomatal index (39.6), highlighting its significant role in regulating transpiration. Stomatal types varied among species: • Anomocytic stomata were observed in Potentilla multifida and Vicia baicalensis. • Anisocytic stomata were found in Delphinium grandiflorum and Ranunculus borealis. • Paracytic stomata were present in Gentiana algida, Adenophora remotiflora, Helianthemum nummularium, Anemone crinita, and Ranunculus acris. Conclution In the study of the structure, form, and number of stomatal cells in saponin-containing plants growing in Mongolia, Anemone crinita Juz. was found to have the highest number of stomatal and epidermal cells, indicating its high efficiency in gas exchange, water regulation, and protection against external stress. Furthermore, Vicia baicalensis (Turcz.) B.Fedtsch. showed the highest stomatal index, confirming its strong capacity for active regulation of gas exchange. The variation in stomatal cell types among plant species was identified as playing an important role in ecological and biological adaptation as well as protective mechanisms.