C2H2 zinc finger protein transcription factor plays an important role in plant growth and development, stress response and regulation of secondary metabolism synthesis. The previous comparative genomic studies between Golden buckwheat and Tartary buckwheat found that the high flavonoid content in Golden buckwheat may be due to the amplification of the gene family related to flavonoid biosynthesis, such as FdCHI, FdF3H and FdDFR. However, C2H2 zinc finger protein transcription factor family genes involved in flavonoid biosynthesis have not been reported in Golden buckwheat. Therefore, genome-wide identification and expression profiling of FdC2H2-ZFP transcription factor in Golden buckwheat were performed in this study. A total of 114 Golden buckwheat FdC2H2-ZFPs were identified. On the basis of RNA-Seq data, the C2H2 zinc finger protein gene FdC2H2-2 was screened and cloned. This gene has three typical C2H2 zinc finger structures and has high homology with AtTREE1 and AtDAZ3. qRT-PCR showed that the expression of FdC2H2-2 gene was significantly induced by jasmonic acid. In addition, the rutin content in the hairy roots of overexpressed FdC2H2-2 was significantly higher than that of the control, and the expressions of flavonol synthase (FLS), phenylalanine ammonlyase (PAL) and flavonoid 3',5' -hydroxylase (F3'5'H), the key enzyme genes in the rutin synthesis pathway, were significantly increased. These results indicate that FdC2H2-2 gene may positively regulate the accumulation of rutin by activating the expressions of the key enzyme genes of rutin biosynthesis, FLS, PAL and F3'5'H. In order to provide reference for exploring the biological function of C2H2 zinc finger protein gene in Golden buckwheat.