Objective: Free-living amoebae, including Acanthamoeba constitute a large group of amoebae that live in fresh water, salty and bitter, moist soil, carious plants, and some on the stool. They are medically important agents. It is a medically important agent. The aim of the present study is to determine the effects of aqueous and alcoholic extracts of Artemisia annuaon trophozoites and cysts of Acanthamoeba in vitro.Methods: In this experimental research, after genotyping the clinical isolate, we prepared the aqueous and alcoholic extracts of Artemisia annua. Various concentrations (1.25, 2.5, 5, and 10 mg/ml) of the aqueous and alcoholic extracts of this plant as well as artemisinin were tested at three different times (24, 48 and 72 h) on trophozoites and cysts of Acanthamoebain vitro. We evaluated viability of the parasite by trypan blue, MTT, and flow cytometry analyses.Results: We observed the anti-acanthamoeba activity of different concentrations of the Artemisia extract. In the presence of 10 mg/ml alcoholic extract in medium culture after 72 h, we observed that 30.51% trophozoites and 91.40% cysts of Acanthamoeba were viable. However, in the presence of 10 mg/ml aqueous extract of Artemisia annua, only 58.25% trophozoites and 81.53% cysts were alive in the in medium culture after 72 h.Conclusion: Aqueous and alcoholic extracts of Artemisia annua had dose- and time dependent anti-acanthamoeba activity.