Geographicdistribution with differences in abiotic and biotic factors may affectprincipal components of medical plant. Representative secondary metabolites of Alpinia oxyphylla Miq. From17 different geographic regions was measured by ultra-fast high performanceliquid chromatography/quadrupole tandem mass spectrometry (UFLC-MS/MS). Wereused for high-throughput RNA sequencing. After RNA-Seq and de novo transcriptomeassembly of 12 libraries prepared from the Capsular fruits of Alpinia oxyphylla from four regions with significantlydifferent on the Representativesecondary metabolites, 260,263 transcripts and 96,342 unigenes wereobtained, 103, 02 genes were annotated of the venn map. Upon the Two pairs ofthe material combination from four different regions, Differentially ExpressedGenes found involved in several physiological processes, e.g., “Flavonoidbiosynthesis”, “Phenylpropanoid biosynthesis”, Sesquiterpenoid and triterpenoidbiosynthesis”, Phenylalanine metabolism Flavone and flavonol biosynthesis”, and“Ubiquinone and other terpenoid-quinone biosynthesis”. A number of genesinvolved in Flavonoid biosynthesis have been identified anddeserve further functional characterization. This study clearly demonstratedthat medical plant from different regions has significant difference on thesecondary metabolites, and understanding of this process may help to select thekey candidate gene and its biosynthesis.