Background: In Mongolia there are over 800 species of medicinal plants, which have advocated in the Indian- Tibetan traditional system of medicine. These species of plants were classified according to their taste, properties, and virtues, and upon this qualification. [1]In Mongolia treatment of diseases are traditionally done using herbal preparations. In general herbal preparations should show similar advantages like synthetic products. It can be assumted that they show low toxicity, soft activity and also a low range of adverse effects. On account of these aspects the use of herbal preparations became more interested in the treatment of different disease within the last decades.Just this more intensive use of herbs increased a problem, which is connected with it: this is standardization and the quality control of herbal preparations with respect to its biological active ingredients.A lot of medicinal plants have being used in science of medicine for a long time. Specifically Rhubarb has a long history. These are named in Chinese and Tibetan hospitals as: jumza, jumgan, shinshin, chubu-rum.[2] Zygophyllum potaninii is grown in the botanical region of trans-Altai, Alash Gobi of the country. It is known as Khulangiin undaa, Argaliin undaa among the people. [3]Purpose of the study: Purpose of our study is to conduct pharmacognostic study on the aerial and lower parts to define important criterion in quality assurance and to work out project of state standard some medicinal plants.Materials and methods of the study: The upper side of Rheum undulatum L were prepared in July, Saihan sum of Bulgan province, Zygophyllum Potaninii Maxim was collected in July Bayan-Ondor sum of Bayanhongor aimag.Microscopic examination of the plant using Enaval lightmicroscopy.Biological active ingredients were identified by thin layer chromatography and ultraviolet spectrum. Silica gel GF 254 (Merck) plates were used for thin layerchromatography. The developed TLC were examinedunder UV 254 nm, UV365 nmAmount of total flavonoids and anthraglycoside were defined by spectrophotometer Unicam 5625. Amount of anthraglycoside draw curve of Kobalt chloride GF-XI according to pharmacopoeian article.Results:1. Leaf of Rheum undulatum has dorsiventral structure, handle has thin wall of surface parenchyma in the middle of leaf parenchyma cell whith large. The leaves of Zygophyllum potaninii are isolateral in structure. Vascular bundle of midrib collateral type is nearly ringed. Anamocytic stomata are on both sides.2. It was determined that anthraquinone compound contained in leaf Rheum undulatum. Leaf anthraquinone compound of Rheum undulatum by 58.4%. In Zygophyllum Potaninii rate of total flavonoid yield contained in medicinal plant material, particle size 2 mm, and concentration of dissolver is 70%, in the most suitable condition total flavonoid was determined 1.38%.References:1. Ligaa,U.Medicinal Plants of Mongolia used in Mongolian traditional medicine. Ulaanbaatar2. Khaidav Ts., Meschikova G.A. Mongolian Medicinalplants.Ulaanbaatar. 19883. Medicinal plants in Mongolian medicine. Ulaanbaatar, 1985