Salinity is a major abiotic stress in plants that causes significant reductions in crop yield. The need for improvement of food production has driven research to understand factors underlying plant responses to salt and mechanisms of salt tolerance. The aim of improving tolerance in traditional crops has been initiated but most crops can only tolerate a limited amount of salt in their systems to survive and produce biomass. Studies of naturally occurring high salt-tolerant plants (halophytes) are now being promoted for economic interests such as food, fodder or ecological reasons. Suaeda fruticosa, a member of the family Chenopodiaceae, belongs to a potential model halophyte genus for studying salt tolerance. However, published reports on the identification of genes, expression patterns and mechanisms of salinity tolerance in succulent halophytes are very limited. Next generation RNA-sequencing techniques are now available to help characterize genes involved in salinity response, along with expression patterns and functions of responsive genes. In this study, we have optimized the assembly of the transcriptome of S. fruticosa. We have annotated the genes based on their gene ontology characteristics and analyzed differential expression to identify genes that are up- and down-regulated in the presence of salt and have grouped the genes based on their putative functions. We also have provided evidence for groups of transcription factors that are involved in salt tolerance of this species and have identified those that may affect the regulation of salt tolerance. This work elucidates the characterization of genes involved in salinity tolerance to increase our understanding of the regulation of salt in a succulent halophyte.