This study provides a comprehensive genomic and transcriptomic analysis of Lagerstroemia indica, a widely cultivated ornamental woody shrub/tree used as a traditional medicinal plant in East Asia and Egypt. The genome of L. indica was sequenced using next-generation sequencing technologies, resulting in an assembled genome of 324.01 Mb, with 98.21% of the sequences placed in 24 pseudo-chromosomes. The genome contains 28,811 protein-coding genes, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs. The genome was found to be hexaploid, with a whole genome triplication occurring approximately 38.5 million years ago. The study identified 137 R2R3 MYB genes, of which ten positively regulate flavonoid/anthocyanin biosynthesis. The colors of the flowers with white, purple (PB), and deep purplish pink (DPB) petals were determined by the levels of delphinidin-based (Dp) derivatives. However, the substrate specificities of LiDFR and LiOMT likely resulted in different compositions of flavonoid/anthocyanin. Two LiTTG1s (LiTTG1-1 and LiTTG1-2) were found to be homologs of AtTTG1 (WD40). LiTTG1-1 was found to repress anthocyanin biosynthesis using the tobacco transient transfection assay. The study also identified several genes, including LiDFR, LiOMTs, and R2R3 LiMYBs, that are related to anthocyanin biosynthesis. The results suggest that L. indica is a palaeohexaploid species, and that LiTTG1-1 represses anthocyanin biosynthesis. The study provides insights into the mechanisms and alleles responsible for flower color development in L. indica. The findings have implications for molecular breeding and the understanding of flavonoid biosynthesis in plants.This study provides a comprehensive genomic and transcriptomic analysis of Lagerstroemia indica, a widely cultivated ornamental woody shrub/tree used as a traditional medicinal plant in East Asia and Egypt. The genome of L. indica was sequenced using next-generation sequencing technologies, resulting in an assembled genome of 324.01 Mb, with 98.21% of the sequences placed in 24 pseudo-chromosomes. The genome contains 28,811 protein-coding genes, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs. The genome was found to be hexaploid, with a whole genome triplication occurring approximately 38.5 million years ago. The study identified 137 R2R3 MYB genes, of which ten positively regulate flavonoid/anthocyanin biosynthesis. The colors of the flowers with white, purple (PB), and deep purplish pink (DPB) petals were determined by the levels of delphinidin-based (Dp) derivatives. However, the substrate specificities of LiDFR and LiOMT likely resulted in different compositions of flavonoid/anthocyanin. Two LiTTG1s (LiTTG1-1 and LiTTG1-2) were found to be homologs of AtTTG1 (WD40). LiTTG1-1 was found to repress anthocyanin biosynthesis using the tobacco transient transfection assay. The study also identified several genes, including LiDFR, LiOMTs, and R2R3 LiMYBs, that are related to anthocyanin biosynthesis. The results suggest that L. indica is a palaeohexaploid species, and that LiTTG1-1 represses anthocyanin biosynthesis. The study provides insights into the mechanisms and alleles responsible for flower color development in L. indica. The findings have implications for molecular breeding and the understanding of flavonoid biosynthesis in plants.