"Long-storage" tomato ( Solanum lycopersicum L.) is a niche product typical of the Mediterranean area, traditionally cultivated under no water supply, the fruits of which combine a good taste with excellent nutritional properties. High-performance liquid chromatography coupled with diode array detection and electron spray-mass spectrometry (HPLC/DAD/ESI-MS) was used to identify the phenolic profile in 10 landraces of long-storage tomato, grown under a typical semiarid climate, as compared to a processing tomato hybrid cultivated in the same environment, under both well-irrigated and unirrigated conditions. Sixteen different secondary metabolites, belonging to the classes of cinnamoylquinic acids and flavonoids, were identified. Quantitative analyses were also performed to monitor the changes in the phenolic content along the batch. The results highlighted that landraces originating from the same area exhibit different fruit morphologies but own a similar biochemical profile. Moreover, the two controls (well irrigated and unirrigated) are placed into the same cluster, suggesting that these secondary metabolites in tomato fruits may be more genetics-dependent than environment-dependent. Given the analysis of phenols nowadays represents a useful tool to assess the genetic variability in tomato, these compounds could be adopted as chemotaxonomic markers in the traceability of this niche product.