Two squalene epoxidase (SE) genes were cloned by reverse transcription polymerase chain reaction (RTPCR) from Tripterygium wilfordii hairy root. The genes are named as TwSE1 (GenBank accession MG717395) and TwSE2 (GenBank accession MG717396). Sequence analysis indicates that the open reading frame of TwSE1 and TwSE2 genes were 1 578 bp and 1 584 bp, which encoding 525 and 527 amino acids. Two amino acid sequences from TwSE1 and TwSE2 shared 76.18% similarity, but were highly divergent in Nterminal regions. Further, gene expression pattern in different tissues and the expression level of TwSE in T. wilfordii hairy root after treatment by methyl jasmonate (MeJA) was detected by realtime PCR. TwSE1 and TwSE2 genes were expressed in roots, stems, young leaves, old leaves and flowers of T. wilfordii. TwSE1 expressed the highest in flowers and lowest in roots, but TwSE2 expressed the highest in flowers and lowest in old leaves. The expression of TwSE2 was lower than that of TwSE1 in all tissues. MeJA treatment enhanced the TwSE1 and TwSE2 expression in hairy roots. The expression level of TwSE1 and TwSE2 has a increasing tendency in the early stage, then decreased in the middle stage and increased in the late time. The highest expression was reached after the treatment of 3 h, then decreased, and the expression level increased rapidly after 12 h. In same treatment condition, the increase of TwSE2 gene expression level was less than that of TwSE1 gene.