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Capparis decidua a medicinal shrub belonging to the family Capparaceae , grows abundantly in wild regions of Asia, Africa, and Saudi Arabia. Due to its medicinal and nutritional value, a study on anatomical and physiological adaptations under various desert habitats was conducted. Results revealed that plants in saline areas showed significant anatomical and physiological modifications particularly in stem and roots show better survival under the harsh saline conditions of the desert. It was noted that the root epidermis thickness was not affected in a slightly saline environment as it showed no significant increasing or decreasing trend in the cross-section of the plant population from non-saline to slightly saline (p > 0.05) while it increased significantly in plants growing at highly saline (p < 0.05). Whereas endodermis cell area differs significantly between plants growing at all selected study sites it increased continuously with a rise in the salinity level of the soil (p < 0.05). Meanwhile, water storage capacity and reduction of water loss in the stem area, epidermis, and sclerenchyma were also recorded. In a highly saline environment, results intimate the deduction of photosynthetic pigments, an increase in total soluble proteins, total free amino acids, total soluble sugars, and proline, and a rise in stem and root tissue Na+, K+, Ca2+, and Cl− contents and meanwhile, accumulation of secondary metabolites (Phenolics and flavonoids). These anatomical and physiological adaptations in natural populations appear to be very important for their better survival in a harsh saline desert environment. It was concluded that C. decidua was found in all different edaphic habitats of the Cholistan Desert, due to its adaptive features, which were very obvious in this plant and highly saline site. • Capparis decidua a medicinal shrub belonging to the family Capparaceae. • Anatomical and physiological adaptations was examined under various desert habitats. • Plants in saline areas showed significant anatomical and physiological modifications. • It was concluded that C. decidua was found in all edaphic habitats of the desert. [ABSTRACT FROM AUTHOR]