Geranylgeranyl-diphosphate synthases (GGDPS) catalyze branch point enzymatic reactions producing isoprenoid-derived products which are necessary for plant growth and responses to a wide range of biotic and abiotic stresses. In our study, full length geranylgeranyl-diphosphate synthase 1 (PgGGDPS1) and 2 (PgGGDPS2) cDNA were isolated and characterized from the flower of Panax ginseng and 4-year old P. ginseng cv. Gumpoong. The cDNA had open reading frame of 1032 and 1116 bp with a deduced amino acid sequence of 343 and 371 residues for GGDPS1 and GGDPS2, respectively. The calculated molecular mass of GGDPS1 and GGDPS2 were approximately 37.66 and 40.21 kDa with a predicated isoelectric point of 5.32 and 6.23 and predicted localization of plastid. A GenBank Blast X search revealed that the deduced amino acid of PgGGDPS1 shared a high degree of homology with GGDPS from Panax notoginseng. The transcription pattern of GGDPS genes was different at various developmental stages. Both GGDPS genes were highly expressed in aerial parts of the plant, especially in rapidly growing tissues such as 4-year old flower and stem tissues. Transcript level of PgGGDPS1 was differentially induced in ginseng not only during Pseudomonas syringae pv tomato infection but also after exposure to abiotic stresses. Our results suggested that the induction of GGDPS genes specifically PgGGDPS1 by drought stress may affect chlorophyll levels, intracellular GA content and accumulation of carotenoids as the precursor for higher production of ABA and possibly stomatal closure as the barrier for water loss.