Tartary buckwheat (Fagopyrum tataricum) is widely planted in the world because of its high nutritional content and strong salt tolerance. However, high salinity still causes some declines in the crop production. In addition, it is unclear of molecular mechanism imparting salt tolerance on this crop. In order to obtain more detailed information regarding this mechanism, we made transcriptome comparisons between short-term acclimation to salt stress (100 mM of NaCl, 48 h) and control in two existing and two new salt-tolerant cultivars of Tartary buckwheat in this study. In total, 205.2 million clean reads were produced through an illumina sequencing approach. A total of 10,865 unigenes were annotated against all four public databases: Nr, Swiss-Prot, KOG and KEGG. 42 common unigenes in all the four cultivars expressed differentially after 100 mM of NaCl for 48 h, suggesting that these differentially expressed unigenes (DEGs) may be involved in salinity response. In addition, we identified 57 transcription factor families total in this study, whereas eight of 42 DEGs can encode this protein. We also observed certain unigenes were ROS (reactive oxygen species) related, including superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX), which were chosen for validation by quantitative real-time PCR. Taken together, the transcriptome data obtained from distinct cultivars of F. tataricum with different salt tolerance was the first report, which provides a valuable insight into the mechanisms of salt tolerance and offers promising references for cultivating strong salt-tolerant Tartary buckwheat cultivars.