Salinity is an ecological factor of considerable importance, affecting a considerable area of irrigation projects in the agricultural fields on the order of 20% to 30%. One of the bioremediation approaches to reclaim saline soil is by employing saline resistant plant or tree accessions, which can adapt to the harsh environments and still be productive. One of the multipurpose trees which are being cultivated by farmers and wood based industries on large scale in Tamilnadu is Casuarina equisetifolia. This species has been a boon to tree cultivation as it has a wide range of ecological adaptability. The tree improvement program on this species has come up with a set of high productive clones of C. equisetifolia which now requires accession site matching so as to support appropriate utilization of waste and unproductive lands. In order to screen Casuarina clones at a nursery stage for saline tolerance is therefore highly significant in facilitating planting activities for saline affected areas. Hence identifying a suitable biochemical marker in combination with morphological and physiological studies conferring saline tolerance in C. equisetifolia was carried out. Six clones collected from Thiruchendur area was used for the study. Among them clone three and six tolerated salinity level up to 200 mM of sodium chloride for a period of 40 days.