Panax ginseng C.A. meyer (family: Araliaceae) is a perennial crop that has been widely used as a traditional medicine in Korea. Various P. ginseng cultivars exhibit a range of morphological and physiological traits as well as genetic diversity. To elucidate the differences of primary metabolism underlying such genetic diverstiy, we performed primary metabolite profiles in adventitious roots from five Panax ginseng cultivars using gas chromatography-mass spectrometry (GC-MS). The GC-MS analysis revealed eight primary metabolites as biomarkers and allowed us to classify the five cultivars into three groups. We selected three cultivars to represent each group and analyzed their transcriptomes by Illumina sequencing. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways. Our data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.