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A study was conducted to investigate structural and functional modifications in three differently adapted ecotypes of Aeluropus lagopoides (Linn.) Trin. ex Thw. under saline conditions. Two ecotypes were collected from moderately saline Bailahwala Dahar (BD) and heavily salt-affected Ladam Sir (LS), respectively while one ecotype was selected from least saline Derawar Fort (DF), which was considered as a control. Vegetative shoots (ramets) of equal size were detached from the mother plant and grown in hydroponic culture solution. Four treatments were maintained during the experiment, viz. 0 (control), 100, 200 and 300 mM NaCl. Ecotype LS showed better growth in terms of morphological features like shoot length, root and shoot fresh and dry biomass, leaf area and number of tillers as well as physiological attributes like net assimilation rate, water use efficiency, turgor potential, root and shoot Ca2+ and accumulation of free proline, than those in ecotypes BD and LS under saline conditions. The root aerenchyma was more prominent in ecotype LS than that in the other ecotypes. In addition, ecotype LS depicted large cortical cells, thick endodermis barrier, high sclerification and large phloem area, all being responsible for efficient conduction of salts and water under saline stress. Structural and functional modifications for salinity tolerance in all three ecotypes were very specific and can be related to their survival under harsh environmental conditions and degree of salt tolerance. Anatomical modifications were the true representatives of habitat ecology of A. lagapoides ecotypes. It is concluded that long-term exposure of A. lagopoides ecotypes to their specific habitats imposed changes in their genetic makeup, which ensure successful survival in their respective habitat. (c) 2018 Friends Science Publishers