Abstract:The flavonoid content in immature leaves was significantly higher than that in mature leaves of Myrciaria cauliflora. In order to understand the information of differentially expressed genes related flavonoid synthesis in M. cauliflora, the transcriptome of 2 kinds of leaves were sequenced by Illumina HiSeq method. The results showed that there were 59 321 Unigenes obtained from young and mature leaves, among which 32 912 unigenes were annotated by 8 databases. There were 77 Unigenes related flavonoid anabolism, and 6 genes were down-regulated significantly in mature leaves, including two CHIs, one CHS, one F3H, one 2-hydroxyiso-flavanone dehydratase gene and one ANS. The RT-PCR verified results of five differentially expressed genes were agreed with the transcriptome sequencing. So, it was suggested that there were a large number of family genes related flavonoid anabolism in the leaves of M. cauliflora, but the decrease of flavonoid content in mature leaves was due to several down-regulated genes.