Artemisia sphaerocephala is one of the excellent sand-fixation plants that can not only well stand up to arid desert environment, but also fix sand and promote desert management, so as to maintain the balance and stability of desert ecosystem. To elucidate the spatial distribution of AM fungi and dark septate endophytes (DSE) and the relativity of AM fungi and DSE with environmental factors associated with the common desert plant A. sphaerocephala, we sampled from three different sites in Inner Mongolia in July 2009, which are north of Hei Chengzi, east of Duo Lun and Yuan Shangdu, respectively. Root samples were collected from four robust A. sphaerocephala, and soil samples were taken from the rhizosphere of A. sphaerocephala in three sites and divided into five depth intervals, 0-10 cm, 10-20 cm, 20-30 cm, 30-40 cm and 40-50 cm respectively. The results showed that the roots of A. sphaerocephala could be highly infected by AM fungi and form a typical type of arbuscular mycorrhizal-Intermediate type (I-type). The distribution and activity of AM fungi were significantly affected by ecological conditions and soil depth and DSE established well symbiosis with rhizosphere of host plant as well. There were significant differences in spore density among the three sites. Spores were the densest in Hei Chengzi site and infecting rate reached the peak at the 0-10cm layer, and then gradually decreased with the increasing of soil depth. The colonization of vesicular in Yuan Shangdu site was higher than that in the other two sites and infecting rate reached the peak at the 10-20cm layer. No significant differences were found in the colonization of DSE and other structures of AM fungi, such as arbuscule, hypha and total colonizations, among different soil layers and different sample sites. There were significant positive correlations between spore density and each soil factors, such as available P, available N, organic matter, urease, acid phosphatase and alkaline phosphatase activity. Vesicular colonization had negative correlations with the activity of soil urease, alkaline phosphatase and acid phosphatase. Soil available N and organic matter had extreme positive correlations with the activity of soil urease, alkaline phosphatase and acid phosphatase (P<0.01). Soil available P was extremely positively correlated with the activity of alkaline phosphatase (P<0.01) and significantly positively correlated with soil urease (P<0.05). However, total colonizations and the colonizations of hyphae, and DSE had not significantly correlated to the soil factors (P>0.05). The formation of arbuscular mycorrhizal may be one of the effective countermeasures for A. sphaerocephala adapting barren drought desert environment. The research results provided basis and references for making full use of AM fungi resources and the foundation for further clarifying the ecological functions of DSE, and indicated that the ecological distribution and abundance of AM fungi and DSE might be a useful index to evaluate soil quality and function of desert ecosystem. Further research should concentrate on going into the dynamics of the relationships among AM fungi, DSE and the roots of the host plant.