This study sequenced and assembled the genome of *Lagerstroemia indica*, a widely cultivated ornamental shrub and traditional medicinal plant. The genome size was determined to be approximately 315-326.43 Mb, with 98.21% of the sequences placed on 24 pseudo-chromosomes. The genome exhibited hexaploidy, with a triplication event occurring around 38.5 million years ago. The study identified 28,811 protein-coding genes, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs. Co-expression analysis revealed that 10 R2R3 MYB genes positively regulate flavonoid/anthocyanin biosynthesis. The colors of white, purple (PB), and deep purplish pink (DPB) petals were found to be determined by the levels of delphinidin-based derivatives. The substrate specificities of LiDFR and LiOMT likely result in different flavonoid/anthocyanin compositions. Two LiTTG1s (LiTTG-1 and LiTTG-1-2) were found to be homologs of AtTTG1 (WD40), with LiTTG-1-1 repressing anthocyanin biosynthesis. This study provides insights into the genome evolution and flavonoid/anthocyanin biosynthesis in *L. indica*.This study sequenced and assembled the genome of *Lagerstroemia indica*, a widely cultivated ornamental shrub and traditional medicinal plant. The genome size was determined to be approximately 315-326.43 Mb, with 98.21% of the sequences placed on 24 pseudo-chromosomes. The genome exhibited hexaploidy, with a triplication event occurring around 38.5 million years ago. The study identified 28,811 protein-coding genes, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs. Co-expression analysis revealed that 10 R2R3 MYB genes positively regulate flavonoid/anthocyanin biosynthesis. The colors of white, purple (PB), and deep purplish pink (DPB) petals were found to be determined by the levels of delphinidin-based derivatives. The substrate specificities of LiDFR and LiOMT likely result in different flavonoid/anthocyanin compositions. Two LiTTG1s (LiTTG-1 and LiTTG-1-2) were found to be homologs of AtTTG1 (WD40), with LiTTG-1-1 repressing anthocyanin biosynthesis. This study provides insights into the genome evolution and flavonoid/anthocyanin biosynthesis in *L. indica*.