The different components of crude mycelium of the predominant endophytic Colletotrichum gloeosporioides of Artemisa annua have been extracted by the methods of acid hydrolysate. We compared the effect of the isolated components on artemisin biosynthesis in hairy root cultures. Therefore, the oligosaccharide elicitor from C. gloeosporioides has been partially purified by column chromatography of Sephadex G25. The isolated oligosaccharide B II (elicitor, MW < 2500) has been revealed to promote the production of artemisinin in Artemisia annua hairy root cultures. When hairy roots of 23-day old cultures (later growth phase) were exposed to the elicitor at 0.4 mg/mL for 4 days, the maximum production of artemisinin reached to 13.51 mg/L, a 51.63% increase over the control. This is the first report on the stimulation of artemisinin production in hairy roots by the oligosaccharide elicitor from an endophytic fungus of A. annua.