This study focuses on the current state of Gentiana tianschanica populations, as well as the floristic composition and ecological characteristics of its populations within the Ile-Alatau region, part of the Ile-Alatau National Park in Almaty Region, Kazakhstan. The genus Gentiana L. is one of the ancient boreal genera that thrived in mixed mountain forests during the Pliocene period. In Kazakhstan, the genus comprises 31 species, including the endemic Gentiana dschungarica Regel. Species of the genus Gentiana L. have been renowned for their medicinal properties since ancient times, particularly in treating gastrointestinal and urogenital disorders, as well as fevers and infectious diseases. In recent years, interest in gentians has increased in both ornamental horticulture and pharmacology. As part of the study, nine natural populations of G. tianschanica were identified and examined in various ecological and phytocoenotic conditions of the Ile-Alatau mountain region. Soil investigations revealed significant differences in the physicochemical properties of soils in the populations' habitats. In the Kimasar Gorge, mountain-meadow chestnut soils with a light loamy composition were observed, whereas the dark chestnut soils of the Big Almaty Gorge showed a high humus content (7.36–18.78%) and elevated levels of key nutrients such as nitrogen (120.4–140.0 mg/kg), phosphorus (58–98 mg/kg), and potassium (470–1000 mg/kg). These findings illustrate the relationship between ecological conditions and the species' adaptation to diverse altitudinal and climatic zones. Phytochemical analysis revealed that G. tianschanica contains valuable bioactive compounds, including phenolic compounds, bitter glycosides, flavonoids, and alkaloids, confirming its high pharmacological significance. The total phenol content ranged from 1567.17 to 9008.20 mg of gallic acid per 100 g of the sample, with the highest concentrations found in the leaves. Total flavonoid content reached up to 1358.25 mg of catechin per 100 g, and vitamin C levels were up to 244.7 mg per 100 g. The most significant compounds identified were syringic acid (up to 1685.8 mg/100 g), quercetin (317.4 mg/100 g), and chlorogenic acid (237.5 mg/100 g), providing potent antioxidant and anti-inflammatory properties. The analysis also demonstrated a high level of antioxidant activity, particularly in the leaves (up to 530.30 mg Trolox per 100 g). These results highlight the potential of G. tianschanica for developing pharmaceutical products with antioxidant and anti-inflammatory properties. However, anthropogenic impacts, including overgrazing, plant collection for decorative and pharmacological purposes, and habitat disturbance, have led to a decline in population density, threatening their conservation. This necessitates the development of comprehensive conservation measures, including monitoring habitat conditions, establishing protective regimes in key areas, and promoting the sustainable use of medicinal plants. The findings of this study reveal the unique ecological and phytochemical adaptations of G. tianschanica to the conditions of various mountainous ecosystems in Kazakhstan. These results are crucial for the conservation of rare and endemic species, the development of pharmaceutical products, and the formulation of ecologically sustainable biodiversity conservation strategies.