Abstract:In order to confirm the molecular basis underlying flower color variegation between Cymbidium hybrid ‘Yufeng’ and its mutant ‘Shangyijinlong’, targeted metabolomics and transcriptomics were used to identify the differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs) involved in flavonoid biosynthesis. The results showed that: (1) by using targeted metabolomics techniques, we identi?ed 38 DEMs,which were significantly enriched in flavonoid biosynthesis, flavone and flavonol biosynthesis. In flavonoid biosynthesis pathway, the contents of phlorizin, xanthohumol, dihydrokaempferol, dihydromyricetin and epigallocatechin were all increased, the contents of naringin and dihydroquercetin were decreased. In addition, the contents of trifolin and quercetin were decreased in flavone and flavonol biosynthesis pathway. (2) Transcriptomics analyses indicated that ?avonoid biosynthesis-related DEGs (CCoAOMT, CHS, CHI, F3H and FLS) were found to be signi?cantly enriched. The results of the transcriptomics were in agreement with the components change of metabolites revealed by metabolomics, it indicated that the color change of ‘Shuangyijinlong’ might be attributed to the down-regulation of CHS、CHI、F3H and FLS that led to blocked of downstream metabolites synthesis. Our results provide reference information for further revealing the molecular regulatory mechanism of color change in Cymbidium hybrid.