Abstract: Artemisia annua releases many kinds of allelochemicals into soils via dead plant residues, either by rain leaching or root exudation. Dead leaves of A. annua contribute more than 80% of the total artemisinin that enters soils during the growth period of A. annua. Allelochemicals released by the dead leaves reduce the growth and yields of succeeding and adjacent crops. Soil microbes play roles in nutrient transformation, organic matter recycling, toxicant decomposition, and hormone efflux, and thus, are important for plant growth and development. However, little is known about the effects of these allelochemicals on soil microorganisms. In these experiments, artemisinin and A. annua leaf litter were each added to soil and changes in microbial biomass and community structure were evaluated. The growth and reproduction of culturable microorganisms in soils showed wide variations in response to A. annua leaf litter or artemisinin. For example, the number of fungi increased but the numbers of actinomycetes, azotobacteria, nitrobacteria, and nitrite bacteria significantly decreased in soils containing A. annua leaf litter or artemisinin. The results suggested that both leaf litter or artemisinin inhibited organic matter mineralization, nitrogen bio-fixation, mobilization of phosphorus and potassium, and nitrification. The soil microbial quotient decreased, while the metabolic quotient increased, after A. annua and artemisinin were added to soils. This result indicated that artemisinin and other allelochemicals in the leaf litter interfered with the metabolism of soil microorganisms. The types and total contents of signature phospholipid fatty acids of microbes such as actinomycetes and protozoa decreased in soils containing leaf litter or artemisinin. The diversity and evenness indices of the microbial community also decreased, suggesting that the soil microbial ecosystem deteriorated as the densities of various microbial groups decreased. Therefore, artemisinin and allelopathic chemicals released from A. annua leaf litter affect the microbial community structure in soils, and may pose a risk to soil ecosystems in the areas where A. annua is widely cultivated. Further research is required to clarify the mechanisms by which allelopathic chemicals from A. annua change the structure of microbial communities in soil.