In the endeavor to enhance the production of pharmaceutically valuable tropane alkaloids including hyoscyamine and scopolamine in Hyoscyamus niger, methyl jasmonate (MeJA) showed significant stimulation both in tropane biosynthetic pathway enzymes activities and tropane alkaloids yields. Therefore it was speculated that genetic engineering of jasmonate biosynthetic pathway might enhance the endogenous jasmonate concentration, followed by stimulating the production of tropane alkaloids. Herein a full-length cDNA encoding allene oxide synthase (AOS, EC 4.2.1.92), the first committed step enzyme in jasmonate biosynthetic pathway was reported (named HnAOS, GenBank accession: EF532599). HnAOS was a novel member of the cytochrome P450 (CYP74A) subfamily. Real-time quantitative PCR analysis showed that HnAOS mRNA accumulated mainly in stems, and responded significantly to wounding or methyl jasmonate.