The squalene synthase (SS) gene from Panax japonicus is an important regulatory enzyme in the biosynthetic pathway of triterpenoid saponins (TS). Regulating the SS activity directly affects the synthesis of squalene (SQ), as well as the synthesis of TS, for which SQ acts as a precursor. By using the homologous cloning program RACE, the SS in the synthetic TS pathway of P. japonicus was successfully cloned , it was named for PjSS. Its fragment was 1353 bp, encoding 415 amino acids. The PjSS protein was an unstable and hydrophobic protein, with the molecular mass of 109559.7 kD. The secondary structure of SS was composed of a-helix, random coil, extended strand, and b-angle of 67.47%, 22.41%, 7.23%, and 2.89%, respectively. The PjSS protein exhibited folding properties to form the typical three-dimensional structure,which has eight functional motifs.RT-PCR indicated that the expressing quantity of PjSS is max in the hypogaeic tuber, the root is second, and the leaf is min.