BACKGROUND: Lagerstroemia indica is an ornamental plant with high economic and ecological values. However, the mechanism underlying the regulation of L. indica petal color variation remains unclear. We used LC-MS/MS and RNA-seq to uncover the genetic basis of flower colour variation with the help of the metabolome and transcriptome of three varieties with different colored petal, 'Huahai', 'Zhuimeng', 'Zixian'. RESULTS: A total of 54 anthocyanidins were identified, 11 peonidin derivatives, 10 cyanidin derivatives, 9 delphinidin derivatives, 5 petunidin derivatives, 5 malvidin derivatives, 4 pelargonidin derivatives, 2 procyanidin derivatives, and 8 other flavonoids. Delphinidin-3-O-glucoside, Malvidin-3-O-glucoside, Petunidin-3-O-glucoside were abundant in petals of all three varieties. 28 differentially accumulated metabolites, including peonidin, cyanidins and flavonoids, were common to 'Zixian' vs. 'Huahai' and 'Zhuimeng' vs. 'Huahai'. Malvidin-3-O-glucoside, Peonidin-3-O-glucoside varied greatly among three varieties. A total of 9923 genes were found to be differentially expressed between red and other colored petals. The upregulation of the expression of ANS (LOC116213234), CHI (LOC116194939), CHI (LOC116196656), F3H (LOC116211316), F3'H (LOC116198721), UGT (LOC104445830) and UGT (LOC116210262) in 'Huahai' was consistent with the contents of cyanidin derivatives, delphinidin derivatives, kaempferol derivatives, naringenin, peonidin derivatives and petunidin derivatives. Regarding transcription factors associated with the anthocyanin pthway, the MYB gene family had the highest number of DEGs, followed by the bHLH gene family, bZIP gene family, WRKY gene family, and MADS box gene family. CONCLUSION: Malvidin-3-O-glucoside and Peonidin-3-O-glucoside may contribute to variation of petal color in the three varieties. The upregulation of ANS, CHI, F3H, F3'H and UGT expression is involved in anthocyanin biosynthesis of the red pigmentation in the L. indica variety. Expression of twelve transcription factor genes has a strongly positive correlation with expression of structural genes. Collectively, our results may facilitate the genetic breeding and cultivation of L. indica with enhanced red pigmentation.