Abstract The variability of metric traits has been studied in 20 Kazakhstan populations of three Nitraria species (N. schoberi L., N. sibirica Pall., and N. komarovii Iljin & Lava ex Bobrov). According to the results, N. sibirica differs from N. schoberi and N. komarovii in small leaves, fruits, and seeds, as well as in the structural features of inflorescences and flowers. N. sibirica is characterized by a greater number of flowers per inflorescence (25–66 on average) than N. schoberi and N. komarovii (14–28 on average). Additionally, N. sibirica differs from N. schoberi by narrower (1.3×) petals and smaller anthers (1.46× in length and 1.2× in width) and pistils (1.25× in length and 1.44× in width). N. komarovii differs from N. schoberi by narrower leaves (1.7×). N. komarovii is characterized by relatively large (especially in width) size of anthers that, together with smaller petals, makes it possible to distinguish this species during flowering. Flowers of N. komarovii are bright yellow, while those in N. schoberi and N. sibirica are white and light purple, respectively. N. komarovii fruits are orange, pale red, or bright red. Fruits of N. schoberi and N. sibirica are dark burgundy and black, respectively. At the intraspecific level, most of the studied metric traits (except for the habitus of N. sibirica plants) are stable and do not depend on the 16 climatic parameters of plant habitats. At the same time, a number of morphological features have been revealed in N. sibirica plants from the Ili Depression. In these populations, N. sibirica plants form shrubs up to 1.8 m in height with a large (up to 90) number of flowers per inflorescence, large petals (3.5 mm in length and 2.2 mm in width on average), small (~0.6 mm) anthers, small (5–5.5 mm in length) fruits, and small (~4 mm in length) narrow ovate stones. These features indicate the ecological–geographical differentiation of N. sibirica under the extra-arid conditions of the stony desert of the depression and evidence a separate taxonomic rank of these populations.