Abstract: Artemisia annua (Qinghao, Asteraceae) is widely grown in Chongqing, China, for extracting the antimalarial drug, artemisinin. Many research studies focus on the release of allelochemicals into soils via leaching with rainfall percolation, on root exudation, and on decomposition of dead plant residues in the growing process of A. annua and on the inhibition of the growth and development of adjacent and subsequent crops by these allelochemicals, particularly artemisinin. Soil microbes play roles in nutrient transformation, organic matter recycling, toxicant decomposition, and hormone efflux, among others. However, little is known about the influence of continuous cultivation of this medicinal plant on soil microorganism populations. Therefore, rhizospheric soils cropped with A. annua for 1, 3, and 5 years were collected and analyzed by routine methods and Illumina MiSeq pyrosequencing to study microbial biomass, enzyme activity and fungal community components. Microbial biomass carbon (C) and nitrogen (N), and enzyme activities (dehydrogenase, urease and invertase) decreased, while C:N in microbes varied, and acid phosphatase activity increased in soils with this medicinal plant compared that in the soil without this plant. These results suggest that allelochemicals released from A. annua into the rhizosphere inhibited the metabolism, growth and reproduction of microorganisms. Principal component coefficients of fungal communities in soils varied significantly, indicating great changes of fungal community structures. In soil fungal communities, Ascomycota was the largest group, accounting for 66.10%-95.28% of the total taxa detected, and there was a significant change in the abundance of both fungal phyla and the top species during A. annua cultivation. Among the predominant fungi, 14 species were found in all soils, and only 1-3 unique species existed in each soil, suggesting that the soil was the most important factor governing the composition of the fungal community, but that community structure is also changed by A. annua cultivation. Erysiphe artemisiae and Puccinia tanaceti, two pathogenic fungi which only infect A. annua, were found in the soils cropped with A. annua. The presence of these two pathogenic fungi in soils would increase the risk of disease incidence in A. annua. Therefore, rotation is advisable when cropping A. annua. Although our study provided some information about fungal community composition and diversity in the soil cropped with A. annua, a large number of microorganisms detected remain unidentified, and the functions of microbes classified is also not clear. The results confirm that the understanding of soil microbial communities remains very poor. Further study should focus on determining the identity and function of bacterial members of the microbial community, as these could be important in maintaining soil quality and function in cropping systems.