Studies conducted to date have shown that Cephalaria uralensis and C. gigantea have high contents of substances with antibacterial, anti-inflammatory, and antioxidant properties; hence, they are attractive plants from the pharmaceutical point of view. However, despite their multifarious desirable biotechnological aspects, the knowledge of these plants is insufficient. The present study focused on the analysis of the morphological, anatomical, and histological structure of aboveground parts of the plants, the identification of the distribution of biologically active compounds in the tissues, and quantitative phytochemical analyses of polyphenolic compounds contained in their aboveground organs. Importantly, the phenological and morphological features of the aboveground organs in the analyzed species were maintained, as in the same plant species growing in different climatic conditions. The analysis of primary metabolites and phenolic compounds in the tissues revealed their distribution in the aboveground organs, which has never been described before. The comparative analyses of the content of total phenolics, total phenolic acids, and total flavonoids in the aboveground organs showed that the level of these substances differed not only between the species but also between the organs. It should be emphasized that the level of these compounds is higher than in many other medicinal plants.