Introduction – Salt stress affects the growth and development of many crops. Citrus is a major global fruit crop and its production is strictly affected by salinity. The use of polyploid citrus rootstocks has been proposed as a strategy to improve salt tolerance. Although tetraploid rootstocks have been found to be more salt tolerant under low and moderate salinity. But, the mechanisms of these dynamics are unknown, including how they compartmentalize the toxic ions under moderate and high saline soils. Materials and methods – Exploring the differences in salt tolerance mechanism between tetraploid and diploid volkamer lemon rootstock, the plants were exposed to moderate (75 mM) and high (150 mM) salinity for 80 days. Various growth parameters (plant height and diameter, leaves number, dry biomass) and various minerals nutrients (N, P, K, Ca, Na and Cl) in leaves and roots of diploid and tetraploid rootstock were studied to understand tolerance mechanism. Results – The results exhibited that tetraploid rootstock behaved differently to cope with the salinity as compared to diploid. In both diploid and tetraploid rootstocks various growth traits were decreased under moderate and high salinity compared to the control. However the decrement was less in tetraploid as compared to diploid rootstocks in moderate and interestingly in high salinity. Conclusion – Tetraploid and diploid rootstocks compartmentalize the toxic ions differentially and/or different parts against moderate and high salt stress. These results suggest that the use of tetraploid citrus rootstocks will be useful and more beneficial for citrus cultivation in moderate and more importantly high saline soils.