In order to explore anthocyanin synthsis regulator genes in Gynura bicolor, the transcriptomes of Gynura bicolor including leaf and flower in control were sequenced by Illumina HiSeq 2500 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 each 22, 16, and 7. (3) According to transcriptome sequencing, the down-expression trend of these 8 anthocyanin synthsis regulator genes agreed with the testing by the RT-PCR. But the trend multiples of these differentially expressed genes by these 2 kinds of approachs were different. So this study included that there are many anthocyanin synthsis regulator genes in Gynura 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.