The giant reed is a fast growing herbaceous non-food crop considered as eligible alternative energy source to reduce the usage of fossil fuels. Tolerance of this plant to abiotic stress has been demonstrated across a range of stressful conditions, thus allowing cultivation in marginal or poorly cultivated land in order not to compromise food security and to overcome land use controversies. In this work, we de novo sequenced, assembled and analyzed the A. donax low G34 ecotype leaf transcriptome (RNAseq analysis) subjected to severe long-term salt stress (256.67 mM NaCl corresponding to 32 dS m-1 electric conductibility). In order to shed light upon the response to high salinity of this non model plant, we analyzed clusters related to salt sensory and signaling transduction, transcription factors, hormone regulation, Reactive Oxygen Species (ROS) scavenging and osmolyte biosynthesis, all of them showing different regulation compared to untreated plants. The analysis of clusters related to ethylene biosynthesis and signaling indicated that gene transcription is modulated towards the minimization of ethylene negative effects upon plant growth. Certainly, the photosynthesis is strongly affected since genes involved in Rubisco biosynthesis and assembly are down-regulated. However, a shift towards C4 photosynthesis is likely to occur as gene regulation is aimed to activate the primary CO2 fixation to PEP (phosphoenolpyruvate). The analysis of "carbon metabolism" category revealed that G34 ecotype under salt stress induces the expression of glycolysis and Krebs cycle related genes, this being consistent with the hypothesis that some sort of salt avoidance might be occurred in A. donax G34 low ecotype. By comparing our results with findings obtained with other giant reed ecotype, we identified several differences in the response to salt that are in accordance with the possibility that heritable phenotypic differences among clones of A. donax might be accumulated especially in ecotypes originating from distant geographical areas, despite their asexual reproduction modality. Additionally, 26,838 simple sequence repeat (SSR) markers were identified and validated. This SSR dataset definitely expands the marker catalogue of A. donax facilitating the genotypic characterization of this species.