In order to explore anthocyanin synthsis regulator genes in Gynura bicolor, we sequenced the transcriptomes of G. bicolor including leaf and flower in control by Illumina HiSeq 2 500 platform. Then, 8 kinds of synthases such as CHS, CHI, F3H, F3′H, F3′5′H, DFR, ANS, 3GT and 3 kinds of transcription factors such as MYB, bHLH and WD40 were retrieved. At the same time, 8 differential expressed genes were identified by the RTPCR. The results showed that: (1) There were 72 unigenes related to anthocyanin synthases, in which 12 differential expressed genes including 1 downregulated F3′H, 2 downregulated 3GTs, 5 downregulated F3Hs and 4 upregulated F3Hs. (2) There were 238 MYBs, 113 bHLHs and 219 WD40s. The differential expressed genes in these 3 kinds of transcription factors were 22, 16 and 7, respectively. (3) According to transcriptome sequencing, the downexpression trend of these 8 anthocyanin synthesis regulator genes agreed with the testing by the RTPCR. But the trend multiples of these differentially expressed genes by these 2 kinds of approaches were different. So this study concluded that there are many anthocyanin synthesis regulator genes in G. bicolor including leaf and flower, but only a few of these genes are significantly different. At the same time, the regulation of transcription factors is more complex than that of synthases.