In recent years, transcriptome analysis based on deep RNA sequencing has been applied to many plants to identify differences in gene expression levels among different cultivars, organs and different treatment conditions (Chen et al. 2014; Yates et al. 2014). In this study, we obtained 189,300 contigs and identified 172,959 unigenes by de novo assembly through RNA-Seq technology in the vegetative and flower buds of C. faberi. According to the Nr protein database, 66,000 (38.16 %) unigenes were successfully annotated. Furthermore, 173 DEGs involved in floral organ development, floral zygomorphy and flowering time were found. These results supported that plant conservative genes, C. faberi-specific genes, and C. faberi tissue-specific genes all were identified in our transcriptomic analysis. Our research will provide valuable information for future study to inquire the flower development mechanisms of C. faberi.