||In this study an efficient procedure has been developed for RNA extraction from buckwheat by CTAB method and the RNA of six samples have been successfully extracted using this method. Then the buckwheat transcriptome was sequenced using the Illumina paired-end sequencing technology. The reads were produced and assembled them into scaffolds, a total of 68,229 unigenes were identified, among which 51363 had significant matches in the Nr database and 35036 had significant matches in the Nt database while 40,086 unigenes had similarity to proteins in the Swiss-Prot database. Altogether, 55,015 unigenes were successfully annotated in the Nr, Nt, Swiss-Prot, KEGG, COG and TrEMBL databases. Finally, 40 CHS genes of buckwheat were obtained from unigene database, and they were divided into three groups based on the homology of sequence. And in order to clarify the differential expression of the CHS sequences in the various parts and the various classes, the homology analysis was performed between each samples, the results show that the CHS gene sequence of sample A has no homology with sample B. Meanwhile, the CHS gene sequences of sample C have just one homology gene with sample D. and the CHS sequences in the roots and the inflorescences have ten homologous sequences. Finally, the CHS sequences were used to study the evolutionary relationships of the various plants, it can be a useful complement to the current plant taxonomy.