Hedysarum L. is one of the large genus of the Fabaceae Lindl. family, consisting of 200 species. Species in the genus Hedysarum are valuable forage and medicinal resources. In this study, we studied Hedysarum theinum Krasnob and Hedysarum neglectum Ledeb growing in the western Altai of Eastern Kazakhstan. H. theinum is a perennial, herbaceous, valuable medicinal plant, a rare species, an Altai-Dzungarian endemic, and a globally endangered species. H. neglectum is a perennial plant of high medicinal and fodder value, growing mainly in the sub-alpine zone. The purpose of the work is to identify the anatomical features and determine the phytochemical composition of the components of two species of Hedysarum. Route-reconnoitering methods were used in a field search of two species of Hedysarum for comparative study in 2020-2021. The extracts were analyzed by gas chromatography with mass spectrometric detection. The location of biologically active substances in the anatomical structure of the stem has been established. Biologically active substances are concentrated around the conductive bundles of the leaf and stem. The comparative anatomical structure of the stem in H. theinum revealed a thick ring of sclerenchyma under the cambium, which is absent in H. neglectum. In determining the phytochemical compounds of the aboveground organs of two Hedysarum species, the total number of components was 74, of which 55 compounds were found in H. theinum and 57 in H. neglectum. In both species, 37 components were detected, in H. neglectum 11 components had significant content, in H. theinum 9 components contained a significant percentage of compounds. Analysis of the root extract showed that H. theinum contains 27 and H. neglectum contains 29 compounds. Of these, 15 compounds are characteristic of both species. The phytochemical data obtained confirm the anti-inflammatory, antibacterial, antifungal, antimicrobial, antimalarial, and antitumor properties of these plants.