Salinity adversely affects plant growth and development, and disturbs intracellular ion homeostasis, resulting in cellular toxicity. Plants that tolerate salinity, halophytes, do so by manifesting numerous physiological and biochemical processes in coordination to alleviate cellular ionic imbalance. The present study was undertaken to analyse the salt tolerance mechanism in Aeluropus lagopoides (L.) trin. Ex Thw. (Poaceae) at both physiological and molecular levels. Plants secreted salt from glands, which eventually produced pristine salt crystals on leaves and leaf sheaths. The rate of salt secretion increased with increasing salt concentration in the growth medium. Osmotic adjustment was mainly achieved by inorganic osmolytes (Na(+)) and at 100 mM NaCl no change was observed in organic osmolytes in comparison to control plants. At 300 mM NaCl and with 150 mM NaCl + 150 mM KCl, the concentration of proline, soluble sugars and amino acids was significantly increased. Transcript profiling of transporter genes revealed differential spatial and temporal expressions in both shoot and root tissues in a manner synchronized towards maintaining ion homeostasis. In shoots, AlHKT2;1 transcript up-regulation was observed at 12 and 24 h in all the treatments, whereas in roots, maximum induction was observed at 48 h with K(+) starvation. The HAK transcript was relatively abundant in shoot tissue with all the treatments. The plasma membrane Na(+)/H(+) antiporter, SOS1, and tonoplast Na(+)/H(+) antiporter, NHX1, were found to be significantly up-regulated in shoot tissue. Our data demonstrate that AlHKT2;1, HAK, SOS1, NHX1 and V-ATPase genes play a pivotal role in regulating the ion homeostasis in A. lagopoides.