The sodium and potassium concentrations in leaf and stem have been genetically studied as physiological components of the vegetative and reproductive development in two populations of F(8) lines, derived from a salt sensitive genotype of Solanum lycopersicum cv. Cerasiforme, as female parent, and two salt tolerant lines, as male parents, from S. pimpinellifolium, the P population (142 lines), and S. cheesmaniae, the C population (116 lines). Genetic parameters of ten traits under salinity and five of them under control conditions were studied by ANOVA, correlation, principal component and QTL analysis to understand the global response of the plant. Two linkage maps including some tomato flowering time and salt tolerance candidate genes encoding for SlSOS1, SlSOS2, SlSOS3, LeNHX1, LeNHX3, were used for the QTL detection. Thirteen and 20 QTLs were detected under salinity in the P and C populations, respectively, and four under control conditions. Highly significant and contributing QTLs (over 40%) for the concentrations of Na(+) and K(+) in stems and leaves have been detected on chromosome 7 in both the populations. This is the only genomic position where the concentration QTLs for both the cations locate together. The proportion of QTLs significantly affected by salinity was larger in the P population (64.3%, including all QTLs detected under control) than in the C population (21.4%), where the estimated genetic component of variance was larger for most traits. A highly significant association between the leaf area and fruit yield under salinity was found only in the C population, which is supported by the location of QTLs for these traits in a common region of chromososome C1. As far as breeding for salt tolerance is concerned, only two sodium QTLs (lnc1.1 and lnc8.1) map in genomic regions of C1 and C8 where fruit yield QTLs are also located but in both the cases the profitable allele corresponds to the salt sensitive, cultivated species. One of those QTLs, lnc1.1 might involve LeNHX3.