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For centuries in Asia, Rhodiola coccinea has been used as a valuable adaptogen medicinal plant known for its remarkable resistance to various stress factors. Physiological tolerance in chloroplasts is believed to be an important factor, which affects the geographic distribution of plant species. However, there is currently no report on how the physiological tolerance in the chloroplasts of R. coccinea varies along an altitudinal gradient in a semi-arid mountain region. In this work, we investigated the physiological variations of the chloroplasts of R. coccinea plants along an altitudinal gradient in the Tianshan Mountains, which are located in northwest China. It was found that the physiological parameters of chloroplasts in R. coccinea plants, including superoxide generation, fatty acid compositions, thylakoid membrane fluidity, chlorophyll a/b ratios and photosynthetic electron transport rates (ETRs), varied nonlinearly with altitude. Indeed, an inflection point was observed at approximately 3,800 m. For altitudes were higher or lower than 3,800 m, the ETR, index of unsaturated fatty acids in the thylakoid membrane and Chl a/b ratios decreased with increasing altitude, whereas the superoxide generation and DPH polarisation of thylakoid membranes increased. In addition, variations in the AsA and GSH contents of chloroplasts could be divided into two distinct phases along the altitudinal gradient. The AsA content slowly decreased with increasing altitudes up to 3,800 m and rapidly decreased above 3,800 m. However, there was a gradual increase in the GSH content between 3,570 and 3,750 m, followed by an abrupt rise to a plateau level. These results demonstrate that the physiological tolerance of chloroplasts widely varies with altitude and have a tight relationship with the range of growth altitude of R. coccinea in Tianshan Mountains.