Soil salinity is a prime impediment in the commercial production of citrus. In the present study two citrus rootstock genotypes viz. Citrus jambhiri and Citrus karna were cultured in vitro and exposed to NaCl salt stress. The previously standardized protocol was used for culture establishment and in vitro shoot and root regeneration. NaCl in different concentrations (25, 50, 75, 100 and 125 mM) was added in standardized regeneration and rooting media to note the biochemical changes due to salinity stress. Results revealed that salinity stress adversely affected the shoot and root differentiation and proved lethal above 100 mM NaCl. The hardening was also hampered due to salt stress. Among different biochemical parameters, proline, total soluble proteins and total sugars accumulation were enhanced however; total chlorophyll content was reduced under salinity stress. The revelation of some new protein polypeptides (21, 26 and 54 kDa) at different increasing salinity levels was attributed to their significance in stress alleviation.