Salinity is a common abiotic stress in many tomato production areas due to the scarcity of fresh water in arid and coastal regions of the world. Therefore, it is necessary to understand the mechanisms underlying genetic diversity for salt sensitivity in order to breed new tolerant cultivars. Several quantitative trait loci (QTLs) related to abiotic stress tolerance have been identified in tomato using genome wide association studies and a few genes underlying them have been successfully identified. In our study, we analysed a whole-genome sequenced panel of 150 tomato genotypes composed of wild accessions (S. pimpinellifollium), cherry tomatoes (S. cerasiforme) and admixed accessions. This panel was phenotyped during early growth and adult stages for both control and salt-stressed treatments. The characterisation of salinity tolerance was achieved on several traits including mineral contents, metabolomics and agronomic traits. A large variability in response was observed for most of the traits and a few tolerant varieties were identified. Then we conducted a genome-wide association study on these traits and identified dozens of QTLs. Several candidate genes within these QTLs have functions related to salinity stress tolerance. Some of them are consistent with previously published QTLs. These results provide new insights into the genetic architecture of tomato salt tolerance and provides new genes to be functionally validated.