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The genus Allium L. (Amaryllidaceae) comprises ecologically flexible species widespread across mountain ecosystems, yet the relationships among morphology, environment, and genetics within section Schoenoprasum in Central Asia remain poorly understood. This study investigated four taxa – A. ledebourianum, A. ivasczenkoae, A. ubinicum, and A. schoenoprasum – from the Kazakhstan Altai to assess their morphological variation, ecological preferences, phytochemical activity, and genetic relationships. Populations occurred on gentle chernozem slopes under humid, nutrient-rich conditions and showed stable regeneration dominated by young individuals. Morphometric analyses revealed pronounced interspecific differentiation: A. ledebourianum attained the greatest height and umbel size, whereas A. ubinicum was smallest but possessed proportionally larger floral organs. Principal component analysis explained 94% of total variance, distinguishing A. ubinicum and A. schoenoprasum from the remaining taxa. Floral traits correlated significantly with temperature, moisture, and soil reaction, indicating strong environmental influence on phenotype. Extract assays showed variable bioactivity, with A. ubinicum displaying the highest antioxidant potential (IC₅₀ = 88 µL) and highest cytotoxicity (LC50 of 5.9 μg/mL), while A. ledebourianum shows no antioxidant activity and the lowest toxicity (LC₅₀ of 10.9 μg/mL). Phylogenetic reconstruction using matK, rbcL, and psbA–trnH chloroplast markers confirmed close affinity between A. ledebourianum and A. ivasczenkoae, while A. ubinicum formed a distinct lineage. Together, morphological, ecological, and molecular data highlight the Kazakhstan Altai as a center of diversification for section Schoenoprasum. These results emphasize the adaptive plasticity of endemic Allium species and their potential as sources of valuable bioactive compounds, underscoring the importance of conserving genetically and morphologically diverse populations in mountain ecosystems.