In order to explore different anthocyanidins and their synthesis regulator genes in Gynura bicolor leaves, we sequenced the transcriptomes of 2 G. bicolors including the purple leaves and the green leaves in control by Illumina HiSeq 2500 platform. At the same time, previously reported 6 kinds of anthocyanidins were detected by HPLC and 6 differential expressed genes were identified by the RTPCR.The aim is to reveal its unique anthocyanidins and key gene information for its synthesis and regulation in G. bicolor. The results showed that: (1) 14 unigenes related to anthocyanidins and 34 unigenes related to their synthesis regulator genes were obtained. There were 6 differential expressed genes from all of these genes between the 2 G. bicolors with purple and green leaves, which were 4 significant downregulated genes including pelargonidin (c11692), cyanidin (c42112), anthocyanidin synthase (c38551), flavonoid 3Oglucosyltransferase (c9064) and 2 significant upregulated genes including dihydroflavonol (c35961), flavonoid 3Oglucosyltransferase (c20283). (2) The up or downexpression trend of these 6 genes agreed very well with the testing by the RTPCR. However, the expression trend by transcriptome sequencing was more significantly different than that by qRTPCR. (3) According to the HPLC detection, the result showed that there were not 4 kinds of anthocyanidins such as delphinidin, peonidin, petunidin and malvidin in G. bicolor. However, the purple leaves had significantly higher content of cyanidin (62.21 mg/kg) than that in green leaves (6.86 mg/kg). At the same time, the content of pelargonidin was below 0.43 mg/kg in 2 G. bicolors. So this study inferred that the reason why the levels of the 2 kinds of anthocyanidins including cyanidin and pelargonidin were decreased significantly in green G. bicolor was the 4 anthocyanin synthesis regulator genes involved in positive regulatory genes like an anthocyanidin synthase and a flavonoid 3Oglucosyltransferase, negative regulatory genes like a dihydroflavonol and a flavonoid 3Oglucosyltransferase.