Oroxylum indicum (L.) Kurz is a medicinally important and rare tree species of the family Bignoniaceae. It is rich in flavonoid content and its mature roots are extensively used in Ayurvedic formulations. O. indicum specific flavonoids like oroxylin B, prunetin and oroxindin possess antibacterial, antiproliferative, antioxidant and anticancerous properties, signifying its importance in modern medicine. In the present study, de novo transcriptome analysis of O. indicum root was performed to elucidate the genes involved in flavonoid metabolism. A total of 24,625,398 high quality reads were assembled into 121,286 transcripts with N50 value 1783. The BLASTx search of 81,002 clustered transcripts against Viridiplantae Uniprot database led to annotation of 46,517 transcripts. Furthermore, Gene ontology (GO) revealed that 34,231 transcripts mapped to 3049 GO terms and KEGG analysis demonstrated that 4570 transcripts plausibly involved in 132 biosynthetic pathways. The transcriptome data indicated that cinnamyl-alcohol dehydrogenase (OinCAD) was abundant in phenylpropanoid pathway genes while; naringenin chalcone synthase (OinCHS), flavone synthase (OinFNS) and flavonoid 3', 5'-methyltransferase (OinF35 MT) were abundant in flavonoid, isoflavonoid, flavone and flavonol biosynthesis pathways, respectively. Transcription factor analysis demonstrated the abundance of MYB, bHLH and WD40 transcription factor families, which regulate the flavonoid biosynthesis. Flavonoid pathway genes displayed differential expression in young and old roots of O. indicum. The transcriptome led to the identification of 31 diverse full length Cytochrome P450 (CYP450) genes which may be involved in biosynthesis of specialized metabolites and flavonoids like baicalein and baicalin. Thus, the information obtained in this study will be a valuable tool for identifying genes and developing system biology approaches for in vitro synthesis of specialized O. indicum metabolites.