Abstract: To obtain the transcriptome database and differentially expressed genes of Citrus grandis 'Tomentosa'(CGT) and Citrus grandis (L.) Osbeck (CGO), three samples of CGT and CGO leaves were collected as test materials. The transcriptome sequencing was performed with the second-generation sequencing method, and the bioinformatic analysis was performed using Nr, Swiss-Prot, KOG, KEGG and other databases. 116 202 Unigenes were assembled and 68 923 genes (59.31%) were annotated. 94 798 genomic expression genes were found in the CGO transcriptome and 107 196 genes in the CGT transcriptome. A total of 6 419 differentially expressed genes (DEGs) were found in CGT and CGO. The results showed that 3 799 DEGs of CGT were up-regulated relative to CGO, accounting for 59.18% and 2 620 DEGs were down-regulated, accounting for 40.82%. Compared with the KEGG database, a total of 771 genes were annotated, involving 125 metabolic pathways, and 9 DEGs related to flavonoids or flavone and flavonol biosynthesis were found. The established transcriptome database of CGT and CGO and the functional annotations of related genes lay a foundation of genetic data for the basic molecular research on the chemical constituents of CGT and CGO.