Transcriptome analysis is an useful tool to discriminate differences in transcript abundance among different cultivars, organs and different treatment conditions in model and non-model plants (Cheung et al. 2006; Trick et al. 2009; Li et al. 2013; Hyun et al. 2014; Zhang et al. 2014). In order to excavate genes that might regulate the floral development in C. faberi, we used high-throughput Illumina sequencing and bioinformatics analysis to compare the de novo transcriptomes of vegetative and flower buds from C. faberi. The vegetative transcriptome can be used to find genes related to the vegetative growth. The floral transcriptome was sufficiently comprehensive for gene discovery and analysis of major metabolic pathways associated with flower traits. Genes expressed differently in the vegetative buds and flower buds may play important roles in the vegetative growth or floral development. Through transcriptome analysis, large numbers of genes related to floral organ initiation, flower symmetry patterning and flowering were identified in C. faberi. These results provide fundamental information for further studies on the molecular mechanism of flower development in C. faberi.