Background : Agastache rugosa (A. rugosa), belonging to the Lamiaceae family, is a medicinal plant mainly distributed in Korea and contains various phenolic compounds revealing anti-fungal and anti-HIV properties. This study is aim to investigate change in phenylpropanoid content of flowers at different developmental stages using high performance liquid chromatography (HPLC) and quantitative real time polymerase chain reaction (qRT-PCR). Methods and Results : The variation in the transcriptional level of phenylpropanoid biosynthetic genes and phenylpropanoid contents in the flowers of A. rugosa at different developmental stages was analyzed. The transcript levels of phenylpropanoid biosynthesis genes, including ArPAL (phenylalanine ammonia-lyase), ArC4H (cinnamate 4-hydroxylase), and ArCHS (Chalcone synthase), were high in flowers at 1st stage compared with flowers at 2nd and 3rd stages. On the other hand, the expression levels of flavonoid biosynthesis genes, including ArTAT (tyrosine amino transferase), ArHPPR (hydroxyl phenylpyruvate reductase), and ArRAS (rosmarinic acid synthase), were higher in flowers at 3rd stage than those of flowers at 1st and 2nd. These results were consistent with HPLC analysis revealing that most phenolic compounds were higher in flowers at 1st and 2nd stage but the level of rosmarinic acid was the highest in 3rd stage. Conclusion : Our findings provide the information on change in phenylpropanoid biosynthesis in A. rugosa flowers at different developmental stages.