Food and nutritional security of a burgeoning global population in face of unabated land degradation, depletion of fresh water and prime croplands, and climate change impacts remains a challenge. Salinization of agricultural lands caused by the natural and anthropogenic factors a severe obstacles to realizing sustainable agricultural production. Majority of the fruit crops are highly susceptible to salinity and related problems like water logging. Use of salt tolerant scion and rootstock cultivars is seen as a viable means of lessening the salt induced damages. Nonetheless, development and commercial release of salt tolerant cultivars in fruit crops has progressed rather slowly. Moreover, salt tolerance of most of the currently available cultivars breaks down when root zone salinity exceeds the critical threshold. This has led to a departure from conventional screening trials to molecular and genomics tools to broaden the understanding of salt stress regulation at the gene, protein and metabolite levels. The ultimate aim is to introgress such genes into established cultivars in a manner that is cost efficient and safe from human and environmental health perspectives.