Squalene synthase (SQS) catalyzes the biosynthesis of squalene by condensing two molecules of farnesyl pyrophosphate (FPP), a key precursor in sterol and triterpene biosynthesis. Previously, we reported that PgSS1 overexpression results in the enhanced biosynthesis of both phytosterols and triterpene saponins in Panax ginseng. Here, cDNAs encoding two new SQS homologs (PgSS2 and PgSS3) from a P. ginseng expressed sequence tag (EST) library are described. Functional complementation analysis revealed that ectopic expression of PgSS1, PgSS2 and PgSS3 in the yeast erg9 mutant strain 2C1 lacking SQS activity restored ergosterol prototrophy. The recombinant mutant yeast produced squalene, squalene epoxide and ergosterol. PgSS1 (mRNA) was highly transcribed in all organs, whereas PgSS2 and PgSS3 (mRNAs) were only transcribed in specific organs. All three genes were activated positively by an elicitor (methyl jasmonate), but their transcriptional patterns were different. In situ hybridization analysis revealed that both PgSS1 and PgSS3 transcripts were preferentially accumulated near conducting tissue in the petiole. The PgSS1 and PgSS3 promoters were isolated, and the tissue- and organ-specific regulation of PgSS genes was examined. Transgenic ginseng was constructed by introducing PgSS1 and PgSS3 promoters fused to the β-glucuronidase (GUS) gene. GUS expression driven by the PgSS1 promoter was found in both roots and shoots, but PgSS3-driven GUS was only found in shoots. These results suggest that the three SQS genes are differently expressed and that all three SQS enzymes are involved in squalene production in P. ginseng.