Panax ginseng root has been used as a major source of ginsenoside throughout the history of oriental medicine. In recent years, scientists have found that all of its biomass, including embryogenic calli and flower buds can contain similar active ingredients with pharmacological functions. In this study, transcriptome analyses were used to identify different gene expressions from embryogenic calli and fl ower buds. In total, 6,226 expressed sequence tags (ESTs) were obtained from cDNA libraries of P. ginseng. Insilico analysis was conducted to annotate the putative sequences using gene ontology functional analysis, Kyoto Encyclopedia of Genes and Genomes orthology biochemical analysis, and interproscan protein functional domain analysis. From the obtained results, genes responsible for growth, pathogenicity, pigments, ginsenoside pathway, and development were discussed. Almost 83.3% of the EST sequence was annotated using one-dimensional insilico analysis.