Abstract: To enrich the genomic information of Ardisia crenata and Ardisia crenata var. bicolor, mature leaves of 2-year-old plants were used as materials. The chromaticity value and pigment content were determined, and transcriptome sequencing analysis was conducted. The results showed that there were obviously differences in leaf color between the two plants. The content of chlorophyll and carotenoids in the leaves of A. crenata were higher than that of A. crenata var. bicolor, while the content of anthocyanins and total flavonoids (except anthocyanins) in the leaves of A. crenata were significantly higher (P<0.05) than that in A. crenata. 549 625 354 original sequences were obtained with transcriptome sequencing, 84 070 unigenes were assembled, and 44 304 unigenes were annotated. Among them, 40 409, 39 034, 27 949, and 32 882 unigenes were annotated in the Nr, KEGG, KOG, and SwissProt database, respectively. A total of 1 558 significantly differentially expressed genes (DEGs) were identified, 610 were upregulated and 948 were downregulated. Four pathways, anthocyanin biosynthesis pathway (ko00942), flavonoid and flavonol biosynthesis pathway (ko00944), flavonoid biosynthesis pathway (ko00941), and carotenoid biosynthesis pathway (ko00906), are closely related to leaf color formation. The transcription factor annotation results showed that the highest number of families were ERF (117 families) and bHLH (104 families). A total of 15 282 SSR loci were identified, and 39 867 pairs of primers were successfully designed for all SSR loci. Therefore, the expression levels of C12RT1, CYP98A2, CHS, CCOAOMT1, CHS2, AOG and CYP707A1 were significantly down-regulated, while At4g26220, TAT, CCOAOMT, Z-ISO and CYP707A2 were significantly up-regulated in 4 pathways, with may affect the color formation of A. crenata var. bicolor leaves.