Salinity stress is a global concern causing huge crop losses which is elevated by global warming and changing climatic conditions. Mango is sensitive to salinity stress. It is essential to understand salinity stress responsiveness in polyembryonic cultivars in order to select a potential cultivars to be used rootstocks. In the present study, one year old seedlings of four polyembryonic cultivars viz., Bappakai, Vellai Colomban, Moovandan and Nekkare were evaluated for their salt stress response under green house conditions. Salinity stress was imposed at 200 mM NaCl concentration. The stress conditions was monitored by recording the soil pH and EC which were found to be > 8.5 and EC > 4.0 dSm-1, respectively under stress conditions. The symptoms of salinity stress like leaf drying from the corners, rolling and drooping were recorded on 24th day of stress. Twenty five DAS soil moisture level reduced by 4 fold from the field capacity under stress in comparison with control (water without salt) indicating moderate drought stress condition, where in the relative water content of the leaves varied among the cultivars which indicated that it is a critical parameter to assess the severity of stress. Among the four cultivars, Nekkare did not show any phenotypic symptoms of salinity stress even after 30 DAS. From this study, the order of salinity susceptibility among the cultivars evaluated is scored as Vellai Colomban > Bappakai > Moovandan > Nekkare, indicating Nekkare is relatively tolerant to salinity stress. Gene expression analysis indicated that there are significant changes in peroxidase system during salinity stress in all the four cultivars. This study is a prelude to work out the dynamics of physiological and molecular responses to salinity stress in mango.